R/getPlinkParam.R
In kindlychung/collr2: QCDH
# TODO: Add comment
#
# Author: kaiyin
###############################################################################
#' Get a list of parameters for passing to plinkr
#'
#' Get a list of parameters for passing to plinkr
#'
#' The parameters of this function corresponds with the parameter of plink, with following rules:
#'
#' 1. "-" replaced by "_"
#'
#' 2. "--" in the beginning removed
#'
#' 3. The parameters "--1" and "--23file" are special cases and corresponds to "one" and "twothreefile" in this function
#'
#' @export
#' @param D Same as plink --D
#' @param K Same as plink --K
#' @param a1_allele Same as plink --a1-allele
#' @param a2_allele Same as plink --a2-allele
#' @param adjust Same as plink --adjust
#' @param all Same as plink --all
#' @param all_pheno Same as plink --all-pheno
#' @param allele1234 Same as plink --allele1234
#' @param alleleACGT Same as plink --alleleACGT
#' @param allele_count Same as plink --allele-count
#' @param allow_extra_chr Same as plink --allow-extra-chr
#' @param allow_no_sex Same as plink --allow-no-sex
#' @param alt_group Same as plink --alt-group
#' @param alt_snp Same as plink --alt-snp
#' @param annotate Same as plink --annotate
#' @param annotate_snp_field Same as plink --annotate-snp-field
#' @param aperm Same as plink --aperm
#' @param assoc Same as plink --assoc
#' @param attrib Same as plink --attrib
#' @param attrib_indiv Same as plink --attrib-indiv
#' @param autosome Same as plink --autosome
#' @param autosome_num Same as plink --autosome-num
#' @param autosome_xy Same as plink --autosome-xy
#' @param bcf Same as plink --bcf
#' @param bd Same as plink --bd
#' @param bed Same as plink --bed
#' @param beta Same as plink --beta
#' @param bfile Same as plink --bfile
#' @param bgen Same as plink --bgen
#' @param biallelic_only Same as plink --biallelic-only
#' @param bim Same as plink --bim
#' @param blocks Same as plink --blocks
#' @param blocks_inform_frac Same as plink --blocks-inform-frac
#' @param blocks_max_kb Same as plink --blocks-max-kb
#' @param blocks_min_maf Same as plink --blocks-min-maf
#' @param blocks_recomb_highci Same as plink --blocks-recomb-highci
#' @param blocks_strong_highci Same as plink --blocks-strong-highci
#' @param blocks_strong_lowci Same as plink --blocks-strong-lowci
#' @param bmerge Same as plink --bmerge
#' @param border Same as plink --border
#' @param bp_space Same as plink --bp-space
#' @param case_only Same as plink --case-only
#' @param cc Same as plink --cc
#' @param cell Same as plink --cell
#' @param cfile Same as plink --cfile
#' @param chap Same as plink --chap
#' @param check_sex Same as plink --check-sex
#' @param chr Same as plink --chr
#' @param chr_set Same as plink --chr-set
#' @param ci Same as plink --ci
#' @param clump Same as plink --clump
#' @param clump_allow_overlap Same as plink --clump-allow-overlap
#' @param clump_annotate Same as plink --clump-annotate
#' @param clump_best Same as plink --clump-best
#' @param clump_field Same as plink --clump-field
#' @param clump_index_first Same as plink --clump-index-first
#' @param clump_kb Same as plink --clump-kb
#' @param clump_p1 Same as plink --clump-p1
#' @param clump_p2 Same as plink --clump-p2
#' @param clump_r2 Same as plink --clump-r2
#' @param clump_range Same as plink --clump-range
#' @param clump_range_border Same as plink --clump-range-border
#' @param clump_replicate Same as plink --clump-replicate
#' @param clump_snp_field Same as plink --clump-snp-field
#' @param clump_verbose Same as plink --clump-verbose
#' @param cluster Same as plink --cluster
#' @param cluster_missing Same as plink --cluster-missing
#' @param cm_map Same as plink --cm-map
#' @param cnv_blue Same as plink --cnv-blue
#' @param cnv_border Same as plink --cnv-border
#' @param cnv_brown Same as plink --cnv-brown
#' @param cnv_check_no_overlap Same as plink --cnv-check-no-overlap
#' @param cnv_count Same as plink --cnv-count
#' @param cnv_del Same as plink --cnv-del
#' @param cnv_disrupt Same as plink --cnv-disrupt
#' @param cnv_drop_no_segment Same as plink --cnv-drop-no-segment
#' @param cnv_dup Same as plink --cnv-dup
#' @param cnv_enrichment_test Same as plink --cnv-enrichment-test
#' @param cnv_exclude Same as plink --cnv-exclude
#' @param cnv_exclude_off_by_1 Same as plink --cnv-exclude-off-by-1
#' @param cnv_freq_excldue_above Same as plink --cnv-freq-excldue-above
#' @param cnv_freq_excldue_below Same as plink --cnv-freq-excldue-below
#' @param cnv_freq_excldue_exact Same as plink --cnv-freq-excldue-exact
#' @param cnv_freq_exclude_above Same as plink --cnv-freq-exclude-above
#' @param cnv_freq_exclude_below Same as plink --cnv-freq-exclude-below
#' @param cnv_freq_exclude_exact Same as plink --cnv-freq-exclude-exact
#' @param cnv_freq_incldue_exact Same as plink --cnv-freq-incldue-exact
#' @param cnv_freq_include_exact Same as plink --cnv-freq-include-exact
#' @param cnv_freq_method2 Same as plink --cnv-freq-method2
#' @param cnv_freq_overlap Same as plink --cnv-freq-overlap
#' @param cnv_green Same as plink --cnv-green
#' @param cnv_indiv_perm Same as plink --cnv-indiv-perm
#' @param cnv_intersect Same as plink --cnv-intersect
#' @param cnv_kb Same as plink --cnv-kb
#' @param cnv_list Same as plink --cnv-list
#' @param cnv_make_map Same as plink --cnv-make-map
#' @param cnv_max_kb Same as plink --cnv-max-kb
#' @param cnv_max_score Same as plink --cnv-max-score
#' @param cnv_max_sites Same as plink --cnv-max-sites
#' @param cnv_overlap Same as plink --cnv-overlap
#' @param cnv_red Same as plink --cnv-red
#' @param cnv_region_overlap Same as plink --cnv-region-overlap
#' @param cnv_report_regions Same as plink --cnv-report-regions
#' @param cnv_score Same as plink --cnv-score
#' @param cnv_seglist Same as plink --cnv-seglist
#' @param cnv_sites Same as plink --cnv-sites
#' @param cnv_subset Same as plink --cnv-subset
#' @param cnv_test Same as plink --cnv-test
#' @param cnv_test_1sided Same as plink --cnv-test-1sided
#' @param cnv_test_2sided Same as plink --cnv-test-2sided
#' @param cnv_test_region Same as plink --cnv-test-region
#' @param cnv_test_window Same as plink --cnv-test-window
#' @param cnv_track Same as plink --cnv-track
#' @param cnv_union_overlap Same as plink --cnv-union-overlap
#' @param cnv_unique Same as plink --cnv-unique
#' @param cnv_verbose_report_regions Same as plink --cnv-verbose-report-regions
#' @param cnv_write Same as plink --cnv-write
#' @param cnv_write_freq Same as plink --cnv-write-freq
#' @param complement_sets Same as plink --complement-sets
#' @param compound_genotypes Same as plink --compound-genotypes
#' @param compress Same as plink --compress
#' @param condition Same as plink --condition
#' @param condition_list Same as plink --condition-list
#' @param consensus_match Same as plink --consensus-match
#' @param const_fid Same as plink --const-fid
#' @param control Same as plink --control
#' @param counts Same as plink --counts
#' @param covar Same as plink --covar
#' @param covar_name Same as plink --covar-name
#' @param covar_number Same as plink --covar-number
#' @param cow Same as plink --cow
#' @param d Same as plink --d
#' @param data Same as plink --data
#' @param debug Same as plink --debug
#' @param decompress Same as plink --decompress
#' @param dfam Same as plink --dfam
#' @param distance Same as plink --distance
#' @param distance_exp Same as plink --distance-exp
#' @param distance_matrix Same as plink --distance-matrix
#' @param dog Same as plink --dog
#' @param dominant Same as plink --dominant
#' @param dosage Same as plink --dosage
#' @param double_id Same as plink --double-id
#' @param dprime Same as plink --dprime
#' @param dummy Same as plink --dummy
#' @param dummy_coding Same as plink --dummy-coding
#' @param each_versus_others Same as plink --each-versus-others
#' @param each_vs_others Same as plink --each-vs-others
#' @param epistasis Same as plink --epistasis
#' @param epistasis_summary_merge Same as plink --epistasis-summary-merge
#' @param exclude Same as plink --exclude
#' @param exclude_before_extract Same as plink --exclude-before-extract
#' @param exclude_snp Same as plink --exclude-snp
#' @param exclude_snps Same as plink --exclude-snps
#' @param extract Same as plink --extract
#' @param fam Same as plink --fam
#' @param family Same as plink --family
#' @param fast_epistasis Same as plink --fast-epistasis
#' @param fid Same as plink --fid
#' @param file Same as plink --file
#' @param fill_missing_a2 Same as plink --fill-missing-a2
#' @param filter Same as plink --filter
#' @param filter_cases Same as plink --filter-cases
#' @param filter_controls Same as plink --filter-controls
#' @param filter_females Same as plink --filter-females
#' @param filter_founders Same as plink --filter-founders
#' @param filter_males Same as plink --filter-males
#' @param filter_nonfounders Same as plink --filter-nonfounders
#' @param fisher Same as plink --fisher
#' @param flip Same as plink --flip
#' @param flip_scan Same as plink --flip-scan
#' @param flip_scan_threshold Same as plink --flip-scan-threshold
#' @param flip_scan_verbose Same as plink --flip-scan-verbose
#' @param flip_scan_window Same as plink --flip-scan-window
#' @param flip_scan_window_kb Same as plink --flip-scan-window-kb
#' @param flip_subset Same as plink --flip-subset
#' @param freq Same as plink --freq
#' @param freqx Same as plink --freqx
#' @param from Same as plink --from
#' @param from_bp Same as plink --from-bp
#' @param from_kb Same as plink --from-kb
#' @param from_mb Same as plink --from-mb
#' @param frqx Same as plink --frqx
#' @param fst Same as plink --fst
#' @param gap Same as plink --gap
#' @param gates Same as plink --gates
#' @param gc Same as plink --gc
#' @param gen Same as plink --gen
#' @param gene Same as plink --gene
#' @param gene_all Same as plink --gene-all
#' @param gene_list Same as plink --gene-list
#' @param gene_list_border Same as plink --gene-list-border
#' @param gene_report Same as plink --gene-report
#' @param gene_report_empty Same as plink --gene-report-empty
#' @param gene_report_snp_field Same as plink --gene-report-snp-field
#' @param gene_subset Same as plink --gene-subset
#' @param genedrop Same as plink --genedrop
#' @param genepi Same as plink --genepi
#' @param geno Same as plink --geno
#' @param genome Same as plink --genome
#' @param genome_full Same as plink --genome-full
#' @param genome_lists Same as plink --genome-lists
#' @param genome_minimal Same as plink --genome-minimal
#' @param genotypic Same as plink --genotypic
#' @param gfile Same as plink --gfile
#' @param gplink Same as plink --gplink
#' @param grm Same as plink --grm
#' @param grm_bin Same as plink --grm-bin
#' @param grm_gz Same as plink --grm-gz
#' @param group_avg Same as plink --group-avg
#' @param groupdist Same as plink --groupdist
#' @param gxe Same as plink --gxe
#' @param hap... Same as plink --hap...
#' @param hap Same as plink --hap
#' @param hap_assoc Same as plink --hap-assoc
#' @param hap_freq Same as plink --hap-freq
#' @param hap_impute Same as plink --hap-impute
#' @param hap_max_phase Same as plink --hap-max-phase
#' @param hap_min_phase_prob Same as plink --hap-min-phase-prob
#' @param hap_miss Same as plink --hap-miss
#' @param hap_phase Same as plink --hap-phase
#' @param hap_phase_wide Same as plink --hap-phase-wide
#' @param hap_pp Same as plink --hap-pp
#' @param hap_snps Same as plink --hap-snps
#' @param hap_tdt Same as plink --hap-tdt
#' @param hap_window Same as plink --hap-window
#' @param hard_call_threshold Same as plink --hard-call-threshold
#' @param hardy2 Same as plink --hardy2
#' @param hardy Same as plink --hardy
#' @param help Same as plink --help
#' @param het Same as plink --het
#' @param hethom Same as plink --hethom
#' @param hide_covar Same as plink --hide-covar
#' @param homog Same as plink --homog
#' @param homozyg Same as plink --homozyg
#' @param homozyg_density Same as plink --homozyg-density
#' @param homozyg_gap Same as plink --homozyg-gap
#' @param homozyg_group Same as plink --homozyg-group
#' @param homozyg_het Same as plink --homozyg-het
#' @param homozyg_include_missing Same as plink --homozyg-include-missing
#' @param homozyg_kb Same as plink --homozyg-kb
#' @param homozyg_match Same as plink --homozyg-match
#' @param homozyg_snp Same as plink --homozyg-snp
#' @param homozyg_verbose Same as plink --homozyg-verbose
#' @param homozyg_window_het Same as plink --homozyg-window-het
#' @param homozyg_window_kb Same as plink --homozyg-window-kb
#' @param homozyg_window_missing Same as plink --homozyg-window-missing
#' @param homozyg_window_snp Same as plink --homozyg-window-snp
#' @param homozyg_window_threshold Same as plink --homozyg-window-threshold
#' @param horse Same as plink --horse
#' @param hwe Same as plink --hwe
#' @param hwe_all Same as plink --hwe-all
#' @param ibc Same as plink --ibc
#' @param ibm Same as plink --ibm
#' @param ibs_matrix Same as plink --ibs-matrix
#' @param ibs_test Same as plink --ibs-test
#' @param id_delim Same as plink --id-delim
#' @param id_dict Same as plink --id-dict
#' @param id_match Same as plink --id-match
#' @param iid Same as plink --iid
#' @param impossible Same as plink --impossible
#' @param impute_sex Same as plink --impute-sex
#' @param ind_major Same as plink --ind-major
#' @param indep Same as plink --indep
#' @param indep_pairphase Same as plink --indep-pairphase
#' @param indep_pairwise Same as plink --indep-pairwise
#' @param independent_effect Same as plink --independent-effect
#' @param indiv_sort Same as plink --indiv-sort
#' @param inter_chr Same as plink --inter-chr
#' @param interaction Same as plink --interaction
#' @param je_cellmin Same as plink --je-cellmin
#' @param keep Same as plink --keep
#' @param keep_allele_order Same as plink --keep-allele-order
#' @param keep_autoconv Same as plink --keep-autoconv
#' @param keep_before_remove Same as plink --keep-before-remove
#' @param keep_cluster_names Same as plink --keep-cluster-names
#' @param keep_clusters Same as plink --keep-clusters
#' @param keep_fam Same as plink --keep-fam
#' @param lambda Same as plink --lambda
#' @param lasso Same as plink --lasso
#' @param lasso_select_covars Same as plink --lasso-select-covars
#' @param ld Same as plink --ld
#' @param ld_snp Same as plink --ld-snp
#' @param ld_snp_list Same as plink --ld-snp-list
#' @param ld_snps Same as plink --ld-snps
#' @param ld_window Same as plink --ld-window
#' @param ld_window_kb Same as plink --ld-window-kb
#' @param ld_window_r2 Same as plink --ld-window-r2
#' @param ld_xchr Same as plink --ld-xchr
#' @param lfile Same as plink --lfile
#' @param liability Same as plink --liability
#' @param linear Same as plink --linear
#' @param list Same as plink --list
#' @param list_23_indels Same as plink --list-23-indels
#' @param list_all Same as plink --list-all
#' @param logistic Same as plink --logistic
#' @param lookup... Same as plink --lookup...
#' @param lookup Same as plink --lookup
#' @param lookup_gene Same as plink --lookup-gene
#' @param lookup_list Same as plink --lookup-list
#' @param loop_assoc Same as plink --loop-assoc
#' @param maf Same as plink --maf
#' @param maf_succ Same as plink --maf-succ
#' @param make_bed Same as plink --make-bed
#' @param make_founders Same as plink --make-founders
#' @param make_grm Same as plink --make-grm
#' @param make_grm_bin Same as plink --make-grm-bin
#' @param make_grm_gz Same as plink --make-grm-gz
#' @param make_just_bim Same as plink --make-just-bim
#' @param make_just_fam Same as plink --make-just-fam
#' @param make_perm_pheno Same as plink --make-perm-pheno
#' @param make_pheno Same as plink --make-pheno
#' @param make_rel Same as plink --make-rel
#' @param make_set Same as plink --make-set
#' @param make_set_border Same as plink --make-set-border
#' @param make_set_collapse_group Same as plink --make-set-collapse-group
#' @param make_set_complement_all Same as plink --make-set-complement-all
#' @param make_set_complement_group Same as plink --make-set-complement-group
#' @param map Same as plink --map
#' @param mat Same as plink --mat
#' @param match Same as plink --match
#' @param match_type Same as plink --match-type
#' @param matrix Same as plink --matrix
#' @param max Same as plink --max
#' @param max_maf Same as plink --max-maf
#' @param mc Same as plink --mc
#' @param mcc Same as plink --mcc
#' @param mcovar Same as plink --mcovar
#' @param mds_cluster Same as plink --mds-cluster
#' @param mds_plot Same as plink --mds-plot
#' @param me Same as plink --me
#' @param me_exclude_one Same as plink --me-exclude-one
#' @param memory Same as plink --memory
#' @param mendel Same as plink --mendel
#' @param mendel_duos Same as plink --mendel-duos
#' @param mendel_multigen Same as plink --mendel-multigen
#' @param merge Same as plink --merge
#' @param merge_equal_pos Same as plink --merge-equal-pos
#' @param merge_list Same as plink --merge-list
#' @param merge_mode Same as plink --merge-mode
#' @param merge_x Same as plink --merge-x
#' @param meta_analysis Same as plink --meta-analysis
#' @param meta_analysis_..._field Same as plink --meta-analysis-...-field
#' @param mfilter Same as plink --mfilter
#' @param mh Same as plink --mh
#' @param mhf Same as plink --mhf
#' @param min Same as plink --min
#' @param mind Same as plink --mind
#' @param mishap_window Same as plink --mishap-window
#' @param missing Same as plink --missing
#' @param missing_code Same as plink --missing-code
#' @param missing_genotype Same as plink --missing-genotype
#' @param missing_phenotype Same as plink --missing-phenotype
#' @param missing_var_code Same as plink --missing-var-code
#' @param mlma Same as plink --mlma
#' @param mlma_loco Same as plink --mlma-loco
#' @param mlma_no_adj_covar Same as plink --mlma-no-adj-covar
#' @param model Same as plink --model
#' @param model_dom Same as plink --model-dom
#' @param model_gen Same as plink --model-gen
#' @param model_rec Same as plink --model-rec
#' @param model_trend Same as plink --model-trend
#' @param mouse Same as plink --mouse
#' @param mperm Same as plink --mperm
#' @param mperm_save Same as plink --mperm-save
#' @param mperm_save_all Same as plink --mperm-save-all
#' @param mpheno Same as plink --mpheno
#' @param must_have_sex Same as plink --must-have-sex
#' @param mwithin Same as plink --mwithin
#' @param neighbour Same as plink --neighbour
#' @param no_fid Same as plink --no-fid
#' @param no_parents Same as plink --no-parents
#' @param no_pheno Same as plink --no-pheno
#' @param no_sex Same as plink --no-sex
#' @param no_snp Same as plink --no-snp
#' @param no_x_sex Same as plink --no-x-sex
#' @param nonfounders Same as plink --nonfounders
#' @param nop Same as plink --nop
#' @param not_chr Same as plink --not-chr
#' @param nudge Same as plink --nudge
#' @param null_group Same as plink --null-group
#' @param null_snp Same as plink --null-snp
#' @param oblig_cluster Same as plink --oblig-cluster
#' @param oblig_clusters Same as plink --oblig-clusters
#' @param oblig_missing Same as plink --oblig-missing
#' @param out Same as plink --out
#' @param output_chr Same as plink --output-chr
#' @param output_missing_genotype Same as plink --output-missing-genotype
#' @param output_missing_phenotype Same as plink --output-missing-phenotype
#' @param oxford_pheno_name Same as plink --oxford-pheno-name
#' @param parallel Same as plink --parallel
#' @param parameters Same as plink --parameters
#' @param parentdt1 Same as plink --parentdt1
#' @param parentdt2 Same as plink --parentdt2
#' @param pat Same as plink --pat
#' @param pca Same as plink --pca
#' @param pca_cluster_names Same as plink --pca-cluster-names
#' @param pca_clusters Same as plink --pca-clusters
#' @param ped Same as plink --ped
#' @param pedigree Same as plink --pedigree
#' @param perm Same as plink --perm
#' @param perm_batch_size Same as plink --perm-batch-size
#' @param perm_count Same as plink --perm-count
#' @param pfilter Same as plink --pfilter
#' @param pheno Same as plink --pheno
#' @param pheno_merge Same as plink --pheno-merge
#' @param pheno_name Same as plink --pheno-name
#' @param pick1 Same as plink --pick1
#' @param plist Same as plink --plist
#' @param poo Same as plink --poo
#' @param pool_size Same as plink --pool-size
#' @param ppc Same as plink --ppc
#' @param ppc_gap Same as plink --ppc-gap
#' @param proxy_... Same as plink --proxy-...
#' @param proxy_assoc Same as plink --proxy-assoc
#' @param proxy_b_kb Same as plink --proxy-b-kb
#' @param proxy_b_maxsnp Same as plink --proxy-b-maxsnp
#' @param proxy_b_r2 Same as plink --proxy-b-r2
#' @param proxy_b_threshold Same as plink --proxy-b-threshold
#' @param proxy_b_window Same as plink --proxy-b-window
#' @param proxy_dosage Same as plink --proxy-dosage
#' @param proxy_drop Same as plink --proxy-drop
#' @param proxy_flanking Same as plink --proxy-flanking
#' @param proxy_geno Same as plink --proxy-geno
#' @param proxy_genotypic_concordance Same as plink --proxy-genotypic-concordance
#' @param proxy_glm Same as plink --proxy-glm
#' @param proxy_impute Same as plink --proxy-impute
#' @param proxy_impute_threshold Same as plink --proxy-impute-threshold
#' @param proxy_kb Same as plink --proxy-kb
#' @param proxy_list Same as plink --proxy-list
#' @param proxy_maf Same as plink --proxy-maf
#' @param proxy_maxsnp Same as plink --proxy-maxsnp
#' @param proxy_mhf Same as plink --proxy-mhf
#' @param proxy_r2 Same as plink --proxy-r2
#' @param proxy_r2_no_filter Same as plink --proxy-r2-no-filter
#' @param proxy_replace Same as plink --proxy-replace
#' @param proxy_show_proxies Same as plink --proxy-show-proxies
#' @param proxy_sub_maxsnp Same as plink --proxy-sub-maxsnp
#' @param proxy_sub_r2 Same as plink --proxy-sub-r2
#' @param proxy_tdt Same as plink --proxy-tdt
#' @param proxy_verbose Same as plink --proxy-verbose
#' @param proxy_window Same as plink --proxy-window
#' @param prune Same as plink --prune
#' @param q_score_file Same as plink --q-score-file
#' @param q_score_range Same as plink --q-score-range
#' @param qfam... Same as plink --qfam...
#' @param qmatch Same as plink --qmatch
#' @param qq_plot Same as plink --qq-plot
#' @param qt Same as plink --qt
#' @param qt_means Same as plink --qt-means
#' @param qual_geno_... Same as plink --qual-geno-...
#' @param qual_geno_max_threshold Same as plink --qual-geno-max-threshold
#' @param qual_geno_scores Same as plink --qual-geno-scores
#' @param qual_geno_threshold Same as plink --qual-geno-threshold
#' @param qual_max_threshold Same as plink --qual-max-threshold
#' @param qual_scores Same as plink --qual-scores
#' @param qual_threshold Same as plink --qual-threshold
#' @param r2 Same as plink --r2
#' @param r Same as plink --r
#' @param range Same as plink --range
#' @param rank Same as plink --rank
#' @param read_dists Same as plink --read-dists
#' @param read_freq Same as plink --read-freq
#' @param read_genome Same as plink --read-genome
#' @param read_genome_list Same as plink --read-genome-list
#' @param read_genome_minimal Same as plink --read-genome-minimal
#' @param recessive Same as plink --recessive
#' @param recode12 Same as plink --recode12
#' @param recode Same as plink --recode
#' @param recodeA Same as plink --recodeA
#' @param recodeAD Same as plink --recodeAD
#' @param recodeHV Same as plink --recodeHV
#' @param recode_allele Same as plink --recode-allele
#' @param recode_beagle Same as plink --recode-beagle
#' @param recode_bimbam Same as plink --recode-bimbam
#' @param recode_fastphase Same as plink --recode-fastphase
#' @param recode_lgen Same as plink --recode-lgen
#' @param recode_rlist Same as plink --recode-rlist
#' @param recode_structure Same as plink --recode-structure
#' @param recode_vcf Same as plink --recode-vcf
#' @param recode_whap Same as plink --recode-whap
#' @param reference Same as plink --reference
#' @param reference_allele Same as plink --reference-allele
#' @param regress_distance Same as plink --regress-distance
#' @param regress_pcs Same as plink --regress-pcs
#' @param regress_rel Same as plink --regress-rel
#' @param rel_check Same as plink --rel-check
#' @param rel_cutoff Same as plink --rel-cutoff
#' @param remove Same as plink --remove
#' @param remove_cluster_names Same as plink --remove-cluster-names
#' @param remove_clusters Same as plink --remove-clusters
#' @param remove_fam Same as plink --remove-fam
#' @param rerun Same as plink --rerun
#' @param rice Same as plink --rice
#' @param sample Same as plink --sample
#' @param score Same as plink --score
#' @param score_no_mean_imputation Same as plink --score-no-mean-imputation
#' @param script Same as plink --script
#' @param seed Same as plink --seed
#' @param set Same as plink --set
#' @param set_by_all Same as plink --set-by-all
#' @param set_collapse_all Same as plink --set-collapse-all
#' @param set_hh_missing Same as plink --set-hh-missing
#' @param set_max Same as plink --set-max
#' @param set_me_missing Same as plink --set-me-missing
#' @param set_missing_nonsnp_ids Same as plink --set-missing-nonsnp-ids
#' @param set_missing_snp_ids Same as plink --set-missing-snp-ids
#' @param set_missing_var_ids Same as plink --set-missing-var-ids
#' @param set_names Same as plink --set-names
#' @param set_p Same as plink --set-p
#' @param set_r2 Same as plink --set-r2
#' @param set_r2_phase Same as plink --set-r2-phase
#' @param set_table Same as plink --set-table
#' @param set_test Same as plink --set-test
#' @param sex Same as plink --sex
#' @param sheep Same as plink --sheep
#' @param show_tags Same as plink --show-tags
#' @param silent Same as plink --silent
#' @param simulate Same as plink --simulate
#' @param simulate_haps Same as plink --simulate-haps
#' @param simulate_label Same as plink --simulate-label
#' @param simulate_missing Same as plink --simulate-missing
#' @param simulate_n Same as plink --simulate-n
#' @param simulate_ncases Same as plink --simulate-ncases
#' @param simulate_ncontrols Same as plink --simulate-ncontrols
#' @param simulate_prevalence Same as plink --simulate-prevalence
#' @param simulate_qt Same as plink --simulate-qt
#' @param simulate_tags Same as plink --simulate-tags
#' @param snp Same as plink --snp
#' @param snps Same as plink --snps
#' @param snps_only Same as plink --snps-only
#' @param specific_haplotype Same as plink --specific-haplotype
#' @param split_x Same as plink --split-x
#' @param standard_beta Same as plink --standard-beta
#' @param subset Same as plink --subset
#' @param swap_parents Same as plink --swap-parents
#' @param swap_sibs Same as plink --swap-sibs
#' @param swap_unrel Same as plink --swap-unrel
#' @param tab Same as plink --tab
#' @param tag_kb Same as plink --tag-kb
#' @param tag_mode2 Same as plink --tag-mode2
#' @param tag_r2 Same as plink --tag-r2
#' @param tail_pheno Same as plink --tail-pheno
#' @param tdt Same as plink --tdt
#' @param test_all Same as plink --test-all
#' @param test_mishap Same as plink --test-mishap
#' @param test_missing Same as plink --test-missing
#' @param test_snp Same as plink --test-snp
#' @param tests Same as plink --tests
#' @param tfam Same as plink --tfam
#' @param tfile Same as plink --tfile
#' @param thin Same as plink --thin
#' @param thin_count Same as plink --thin-count
#' @param threads Same as plink --threads
#' @param to Same as plink --to
#' @param to_bp Same as plink --to-bp
#' @param to_kb Same as plink --to-kb
#' @param to_mb Same as plink --to-mb
#' @param tped Same as plink --tped
#' @param transpose Same as plink --transpose
#' @param trend Same as plink --trend
#' @param tucc Same as plink --tucc
#' @param twolocus Same as plink --twolocus
#' @param unbounded Same as plink --unbounded
#' @param unrelated_heritability Same as plink --unrelated-heritability
#' @param update_alleles Same as plink --update-alleles
#' @param update_chr Same as plink --update-chr
#' @param update_cm Same as plink --update-cm
#' @param update_ids Same as plink --update-ids
#' @param update_map Same as plink --update-map
#' @param update_name Same as plink --update-name
#' @param update_parents Same as plink --update-parents
#' @param update_sex Same as plink --update-sex
#' @param vcf Same as plink --vcf
#' @param vcf_filter Same as plink --vcf-filter
#' @param vcf_half_call Same as plink --vcf-half-call
#' @param vcf_idspace_to Same as plink --vcf-idspace-to
#' @param vcf_min_qual Same as plink --vcf-min-qual
#' @param vegas Same as plink --vegas
#' @param version Same as plink --version
#' @param vif Same as plink --vif
#' @param whap Same as plink --whap
#' @param window Same as plink --window
#' @param with_freqs Same as plink --with-freqs
#' @param with_phenotype Same as plink --with-phenotype
#' @param with_reference Same as plink --with-reference
#' @param within Same as plink --within
#' @param write_cluster Same as plink --write-cluster
#' @param write_covar Same as plink --write-covar
#' @param write_dosage Same as plink --write-dosage
#' @param write_set Same as plink --write-set
#' @param write_set_r2 Same as plink --write-set-r2
#' @param write_snplist Same as plink --write-snplist
#' @param xchr_model Same as plink --xchr-model
#' @param zero_cluster Same as plink --zero-cluster
#' @param zero_cms Same as plink --zero-cms
#' @param one Same as plink --1
#' @param twothreefile Same as plink --23file
#' @param wait Logical. If FALSE, the plink process will fork into the background.
#' @param stdout Passed to system2, see its documentation.
#' @param stderr Passed to system2, see its documentation.
#' @param plinkcollFileStems A character vector of all bed file stems you want to pass to plink.
getPlinkParam = function(
D=NULL,
K=NULL,
a1_allele=NULL,
a2_allele=NULL,
adjust=NULL,
all=NULL,
all_pheno=NULL,
allele1234=NULL,
alleleACGT=NULL,
allele_count=NULL,
allow_extra_chr=NULL,
allow_no_sex=NULL,
alt_group=NULL,
alt_snp=NULL,
annotate=NULL,
annotate_snp_field=NULL,
aperm=NULL,
assoc=NULL,
attrib=NULL,
attrib_indiv=NULL,
autosome=NULL,
autosome_num=NULL,
autosome_xy=NULL,
bcf=NULL,
bd=NULL,
bed=NULL,
beta=NULL,
bfile=NULL,
bgen=NULL,
biallelic_only=NULL,
bim=NULL,
blocks=NULL,
blocks_inform_frac=NULL,
blocks_max_kb=NULL,
blocks_min_maf=NULL,
blocks_recomb_highci=NULL,
blocks_strong_highci=NULL,
blocks_strong_lowci=NULL,
bmerge=NULL,
border=NULL,
bp_space=NULL,
case_only=NULL,
cc=NULL,
cell=NULL,
cfile=NULL,
chap=NULL,
check_sex=NULL,
chr=NULL,
chr_set=NULL,
ci=NULL,
clump=NULL,
clump_allow_overlap=NULL,
clump_annotate=NULL,
clump_best=NULL,
clump_field=NULL,
clump_index_first=NULL,
clump_kb=NULL,
clump_p1=NULL,
clump_p2=NULL,
clump_r2=NULL,
clump_range=NULL,
clump_range_border=NULL,
clump_replicate=NULL,
clump_snp_field=NULL,
clump_verbose=NULL,
cluster=NULL,
cluster_missing=NULL,
cm_map=NULL,
cnv_blue=NULL,
cnv_border=NULL,
cnv_brown=NULL,
cnv_check_no_overlap=NULL,
cnv_count=NULL,
cnv_del=NULL,
cnv_disrupt=NULL,
cnv_drop_no_segment=NULL,
cnv_dup=NULL,
cnv_enrichment_test=NULL,
cnv_exclude=NULL,
cnv_exclude_off_by_1=NULL,
cnv_freq_excldue_above=NULL,
cnv_freq_excldue_below=NULL,
cnv_freq_excldue_exact=NULL,
cnv_freq_exclude_above=NULL,
cnv_freq_exclude_below=NULL,
cnv_freq_exclude_exact=NULL,
cnv_freq_incldue_exact=NULL,
cnv_freq_include_exact=NULL,
cnv_freq_method2=NULL,
cnv_freq_overlap=NULL,
cnv_green=NULL,
cnv_indiv_perm=NULL,
cnv_intersect=NULL,
cnv_kb=NULL,
cnv_list=NULL,
cnv_make_map=NULL,
cnv_max_kb=NULL,
cnv_max_score=NULL,
cnv_max_sites=NULL,
cnv_overlap=NULL,
cnv_red=NULL,
cnv_region_overlap=NULL,
cnv_report_regions=NULL,
cnv_score=NULL,
cnv_seglist=NULL,
cnv_sites=NULL,
cnv_subset=NULL,
cnv_test=NULL,
cnv_test_1sided=NULL,
cnv_test_2sided=NULL,
cnv_test_region=NULL,
cnv_test_window=NULL,
cnv_track=NULL,
cnv_union_overlap=NULL,
cnv_unique=NULL,
cnv_verbose_report_regions=NULL,
cnv_write=NULL,
cnv_write_freq=NULL,
complement_sets=NULL,
compound_genotypes=NULL,
compress=NULL,
condition=NULL,
condition_list=NULL,
consensus_match=NULL,
const_fid=NULL,
control=NULL,
counts=NULL,
covar=NULL,
covar_name=NULL,
covar_number=NULL,
cow=NULL,
d=NULL,
data=NULL,
debug=NULL,
decompress=NULL,
dfam=NULL,
distance=NULL,
distance_exp=NULL,
distance_matrix=NULL,
dog=NULL,
dominant=NULL,
dosage=NULL,
double_id=NULL,
dprime=NULL,
dummy=NULL,
dummy_coding=NULL,
each_versus_others=NULL,
each_vs_others=NULL,
epistasis=NULL,
epistasis_summary_merge=NULL,
exclude=NULL,
exclude_before_extract=NULL,
exclude_snp=NULL,
exclude_snps=NULL,
extract=NULL,
fam=NULL,
family=NULL,
fast_epistasis=NULL,
fid=NULL,
file=NULL,
fill_missing_a2=NULL,
filter=NULL,
filter_cases=NULL,
filter_controls=NULL,
filter_females=NULL,
filter_founders=NULL,
filter_males=NULL,
filter_nonfounders=NULL,
fisher=NULL,
flip=NULL,
flip_scan=NULL,
flip_scan_threshold=NULL,
flip_scan_verbose=NULL,
flip_scan_window=NULL,
flip_scan_window_kb=NULL,
flip_subset=NULL,
freq=NULL,
freqx=NULL,
from=NULL,
from_bp=NULL,
from_kb=NULL,
from_mb=NULL,
frqx=NULL,
fst=NULL,
gap=NULL,
gates=NULL,
gc=NULL,
gen=NULL,
gene=NULL,
gene_all=NULL,
gene_list=NULL,
gene_list_border=NULL,
gene_report=NULL,
gene_report_empty=NULL,
gene_report_snp_field=NULL,
gene_subset=NULL,
genedrop=NULL,
genepi=NULL,
geno=NULL,
genome=NULL,
genome_full=NULL,
genome_lists=NULL,
genome_minimal=NULL,
genotypic=NULL,
gfile=NULL,
gplink=NULL,
grm=NULL,
grm_bin=NULL,
grm_gz=NULL,
group_avg=NULL,
groupdist=NULL,
gxe=NULL,
hap...=NULL,
hap=NULL,
hap_assoc=NULL,
hap_freq=NULL,
hap_impute=NULL,
hap_max_phase=NULL,
hap_min_phase_prob=NULL,
hap_miss=NULL,
hap_phase=NULL,
hap_phase_wide=NULL,
hap_pp=NULL,
hap_snps=NULL,
hap_tdt=NULL,
hap_window=NULL,
hard_call_threshold=NULL,
hardy2=NULL,
hardy=NULL,
help=NULL,
het=NULL,
hethom=NULL,
hide_covar=NULL,
homog=NULL,
homozyg=NULL,
homozyg_density=NULL,
homozyg_gap=NULL,
homozyg_group=NULL,
homozyg_het=NULL,
homozyg_include_missing=NULL,
homozyg_kb=NULL,
homozyg_match=NULL,
homozyg_snp=NULL,
homozyg_verbose=NULL,
homozyg_window_het=NULL,
homozyg_window_kb=NULL,
homozyg_window_missing=NULL,
homozyg_window_snp=NULL,
homozyg_window_threshold=NULL,
horse=NULL,
hwe=NULL,
hwe_all=NULL,
ibc=NULL,
ibm=NULL,
ibs_matrix=NULL,
ibs_test=NULL,
id_delim=NULL,
id_dict=NULL,
id_match=NULL,
iid=NULL,
impossible=NULL,
impute_sex=NULL,
ind_major=NULL,
indep=NULL,
indep_pairphase=NULL,
indep_pairwise=NULL,
independent_effect=NULL,
indiv_sort=NULL,
inter_chr=NULL,
interaction=NULL,
je_cellmin=NULL,
keep=NULL,
keep_allele_order=NULL,
keep_autoconv=NULL,
keep_before_remove=NULL,
keep_cluster_names=NULL,
keep_clusters=NULL,
keep_fam=NULL,
lambda=NULL,
lasso=NULL,
lasso_select_covars=NULL,
ld=NULL,
ld_snp=NULL,
ld_snp_list=NULL,
ld_snps=NULL,
ld_window=NULL,
ld_window_kb=NULL,
ld_window_r2=NULL,
ld_xchr=NULL,
lfile=NULL,
liability=NULL,
linear=NULL,
list=NULL,
list_23_indels=NULL,
list_all=NULL,
logistic=NULL,
lookup...=NULL,
lookup=NULL,
lookup_gene=NULL,
lookup_list=NULL,
loop_assoc=NULL,
maf=NULL,
maf_succ=NULL,
make_bed=NULL,
make_founders=NULL,
make_grm=NULL,
make_grm_bin=NULL,
make_grm_gz=NULL,
make_just_bim=NULL,
make_just_fam=NULL,
make_perm_pheno=NULL,
make_pheno=NULL,
make_rel=NULL,
make_set=NULL,
make_set_border=NULL,
make_set_collapse_group=NULL,
make_set_complement_all=NULL,
make_set_complement_group=NULL,
map=NULL,
mat=NULL,
match=NULL,
match_type=NULL,
matrix=NULL,
max=NULL,
max_maf=NULL,
mc=NULL,
mcc=NULL,
mcovar=NULL,
mds_cluster=NULL,
mds_plot=NULL,
me=NULL,
me_exclude_one=NULL,
memory=NULL,
mendel=NULL,
mendel_duos=NULL,
mendel_multigen=NULL,
merge=NULL,
merge_equal_pos=NULL,
merge_list=NULL,
merge_mode=NULL,
merge_x=NULL,
meta_analysis=NULL,
meta_analysis_..._field=NULL,
mfilter=NULL,
mh=NULL,
mhf=NULL,
min=NULL,
mind=NULL,
mishap_window=NULL,
missing=NULL,
missing_code=NULL,
missing_genotype=NULL,
missing_phenotype=NULL,
missing_var_code=NULL,
mlma=NULL,
mlma_loco=NULL,
mlma_no_adj_covar=NULL,
model=NULL,
model_dom=NULL,
model_gen=NULL,
model_rec=NULL,
model_trend=NULL,
mouse=NULL,
mperm=NULL,
mperm_save=NULL,
mperm_save_all=NULL,
mpheno=NULL,
must_have_sex=NULL,
mwithin=NULL,
neighbour=NULL,
no_fid=NULL,
no_parents=NULL,
no_pheno=NULL,
no_sex=NULL,
no_snp=NULL,
no_x_sex=NULL,
nonfounders=NULL,
nop=NULL,
not_chr=NULL,
nudge=NULL,
null_group=NULL,
null_snp=NULL,
oblig_cluster=NULL,
oblig_clusters=NULL,
oblig_missing=NULL,
out=NULL,
output_chr=NULL,
output_missing_genotype=NULL,
output_missing_phenotype=NULL,
oxford_pheno_name=NULL,
parallel=NULL,
parameters=NULL,
parentdt1=NULL,
parentdt2=NULL,
pat=NULL,
pca=NULL,
pca_cluster_names=NULL,
pca_clusters=NULL,
ped=NULL,
pedigree=NULL,
perm=NULL,
perm_batch_size=NULL,
perm_count=NULL,
pfilter=NULL,
pheno=NULL,
pheno_merge=NULL,
pheno_name=NULL,
pick1=NULL,
plist=NULL,
poo=NULL,
pool_size=NULL,
ppc=NULL,
ppc_gap=NULL,
proxy_...=NULL,
proxy_assoc=NULL,
proxy_b_kb=NULL,
proxy_b_maxsnp=NULL,
proxy_b_r2=NULL,
proxy_b_threshold=NULL,
proxy_b_window=NULL,
proxy_dosage=NULL,
proxy_drop=NULL,
proxy_flanking=NULL,
proxy_geno=NULL,
proxy_genotypic_concordance=NULL,
proxy_glm=NULL,
proxy_impute=NULL,
proxy_impute_threshold=NULL,
proxy_kb=NULL,
proxy_list=NULL,
proxy_maf=NULL,
proxy_maxsnp=NULL,
proxy_mhf=NULL,
proxy_r2=NULL,
proxy_r2_no_filter=NULL,
proxy_replace=NULL,
proxy_show_proxies=NULL,
proxy_sub_maxsnp=NULL,
proxy_sub_r2=NULL,
proxy_tdt=NULL,
proxy_verbose=NULL,
proxy_window=NULL,
prune=NULL,
q_score_file=NULL,
q_score_range=NULL,
qfam...=NULL,
qmatch=NULL,
qq_plot=NULL,
qt=NULL,
qt_means=NULL,
qual_geno_...=NULL,
qual_geno_max_threshold=NULL,
qual_geno_scores=NULL,
qual_geno_threshold=NULL,
qual_max_threshold=NULL,
qual_scores=NULL,
qual_threshold=NULL,
r2=NULL,
r=NULL,
range=NULL,
rank=NULL,
read_dists=NULL,
read_freq=NULL,
read_genome=NULL,
read_genome_list=NULL,
read_genome_minimal=NULL,
recessive=NULL,
recode12=NULL,
recode=NULL,
recodeA=NULL,
recodeAD=NULL,
recodeHV=NULL,
recode_allele=NULL,
recode_beagle=NULL,
recode_bimbam=NULL,
recode_fastphase=NULL,
recode_lgen=NULL,
recode_rlist=NULL,
recode_structure=NULL,
recode_vcf=NULL,
recode_whap=NULL,
reference=NULL,
reference_allele=NULL,
regress_distance=NULL,
regress_pcs=NULL,
regress_rel=NULL,
rel_check=NULL,
rel_cutoff=NULL,
remove=NULL,
remove_cluster_names=NULL,
remove_clusters=NULL,
remove_fam=NULL,
rerun=NULL,
rice=NULL,
sample=NULL,
score=NULL,
score_no_mean_imputation=NULL,
script=NULL,
seed=NULL,
set=NULL,
set_by_all=NULL,
set_collapse_all=NULL,
set_hh_missing=NULL,
set_max=NULL,
set_me_missing=NULL,
set_missing_nonsnp_ids=NULL,
set_missing_snp_ids=NULL,
set_missing_var_ids=NULL,
set_names=NULL,
set_p=NULL,
set_r2=NULL,
set_r2_phase=NULL,
set_table=NULL,
set_test=NULL,
sex=NULL,
sheep=NULL,
show_tags=NULL,
silent=NULL,
simulate=NULL,
simulate_haps=NULL,
simulate_label=NULL,
simulate_missing=NULL,
simulate_n=NULL,
simulate_ncases=NULL,
simulate_ncontrols=NULL,
simulate_prevalence=NULL,
simulate_qt=NULL,
simulate_tags=NULL,
snp=NULL,
snps=NULL,
snps_only=NULL,
specific_haplotype=NULL,
split_x=NULL,
standard_beta=NULL,
subset=NULL,
swap_parents=NULL,
swap_sibs=NULL,
swap_unrel=NULL,
tab=NULL,
tag_kb=NULL,
tag_mode2=NULL,
tag_r2=NULL,
tail_pheno=NULL,
tdt=NULL,
test_all=NULL,
test_mishap=NULL,
test_missing=NULL,
test_snp=NULL,
tests=NULL,
tfam=NULL,
tfile=NULL,
thin=NULL,
thin_count=NULL,
threads=NULL,
to=NULL,
to_bp=NULL,
to_kb=NULL,
to_mb=NULL,
tped=NULL,
transpose=NULL,
trend=NULL,
tucc=NULL,
twolocus=NULL,
unbounded=NULL,
unrelated_heritability=NULL,
update_alleles=NULL,
update_chr=NULL,
update_cm=NULL,
update_ids=NULL,
update_map=NULL,
update_name=NULL,
update_parents=NULL,
update_sex=NULL,
vcf=NULL,
vcf_filter=NULL,
vcf_half_call=NULL,
vcf_idspace_to=NULL,
vcf_min_qual=NULL,
vegas=NULL,
version=NULL,
vif=NULL,
whap=NULL,
window=NULL,
with_freqs=NULL,
with_phenotype=NULL,
with_reference=NULL,
within=NULL,
write_cluster=NULL,
write_covar=NULL,
write_dosage=NULL,
write_set=NULL,
write_set_r2=NULL,
write_snplist=NULL,
xchr_model=NULL,
zero_cluster=NULL,
zero_cms=NULL,
one = NULL,
twothreefile = NULL,
wait=TRUE,
stdout="",
stderr="",
plinkcollFileStems=NULL
) {
argList = as.list(match.call())[-1]
argList
}
kindlychung/collr2 documentation built on May 20, 2019, 9:57 a.m.
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# TODO: Add comment
#
# Author: kaiyin
###############################################################################
#' Get a list of parameters for passing to plinkr
#'
#' Get a list of parameters for passing to plinkr
#'
#' The parameters of this function corresponds with the parameter of plink, with following rules:
#'
#' 1. "-" replaced by "_"
#'
#' 2. "--" in the beginning removed
#'
#' 3. The parameters "--1" and "--23file" are special cases and corresponds to "one" and "twothreefile" in this function
#'
#' @export
#' @param D Same as plink --D
#' @param K Same as plink --K
#' @param a1_allele Same as plink --a1-allele
#' @param a2_allele Same as plink --a2-allele
#' @param adjust Same as plink --adjust
#' @param all Same as plink --all
#' @param all_pheno Same as plink --all-pheno
#' @param allele1234 Same as plink --allele1234
#' @param alleleACGT Same as plink --alleleACGT
#' @param allele_count Same as plink --allele-count
#' @param allow_extra_chr Same as plink --allow-extra-chr
#' @param allow_no_sex Same as plink --allow-no-sex
#' @param alt_group Same as plink --alt-group
#' @param alt_snp Same as plink --alt-snp
#' @param annotate Same as plink --annotate
#' @param annotate_snp_field Same as plink --annotate-snp-field
#' @param aperm Same as plink --aperm
#' @param assoc Same as plink --assoc
#' @param attrib Same as plink --attrib
#' @param attrib_indiv Same as plink --attrib-indiv
#' @param autosome Same as plink --autosome
#' @param autosome_num Same as plink --autosome-num
#' @param autosome_xy Same as plink --autosome-xy
#' @param bcf Same as plink --bcf
#' @param bd Same as plink --bd
#' @param bed Same as plink --bed
#' @param beta Same as plink --beta
#' @param bfile Same as plink --bfile
#' @param bgen Same as plink --bgen
#' @param biallelic_only Same as plink --biallelic-only
#' @param bim Same as plink --bim
#' @param blocks Same as plink --blocks
#' @param blocks_inform_frac Same as plink --blocks-inform-frac
#' @param blocks_max_kb Same as plink --blocks-max-kb
#' @param blocks_min_maf Same as plink --blocks-min-maf
#' @param blocks_recomb_highci Same as plink --blocks-recomb-highci
#' @param blocks_strong_highci Same as plink --blocks-strong-highci
#' @param blocks_strong_lowci Same as plink --blocks-strong-lowci
#' @param bmerge Same as plink --bmerge
#' @param border Same as plink --border
#' @param bp_space Same as plink --bp-space
#' @param case_only Same as plink --case-only
#' @param cc Same as plink --cc
#' @param cell Same as plink --cell
#' @param cfile Same as plink --cfile
#' @param chap Same as plink --chap
#' @param check_sex Same as plink --check-sex
#' @param chr Same as plink --chr
#' @param chr_set Same as plink --chr-set
#' @param ci Same as plink --ci
#' @param clump Same as plink --clump
#' @param clump_allow_overlap Same as plink --clump-allow-overlap
#' @param clump_annotate Same as plink --clump-annotate
#' @param clump_best Same as plink --clump-best
#' @param clump_field Same as plink --clump-field
#' @param clump_index_first Same as plink --clump-index-first
#' @param clump_kb Same as plink --clump-kb
#' @param clump_p1 Same as plink --clump-p1
#' @param clump_p2 Same as plink --clump-p2
#' @param clump_r2 Same as plink --clump-r2
#' @param clump_range Same as plink --clump-range
#' @param clump_range_border Same as plink --clump-range-border
#' @param clump_replicate Same as plink --clump-replicate
#' @param clump_snp_field Same as plink --clump-snp-field
#' @param clump_verbose Same as plink --clump-verbose
#' @param cluster Same as plink --cluster
#' @param cluster_missing Same as plink --cluster-missing
#' @param cm_map Same as plink --cm-map
#' @param cnv_blue Same as plink --cnv-blue
#' @param cnv_border Same as plink --cnv-border
#' @param cnv_brown Same as plink --cnv-brown
#' @param cnv_check_no_overlap Same as plink --cnv-check-no-overlap
#' @param cnv_count Same as plink --cnv-count
#' @param cnv_del Same as plink --cnv-del
#' @param cnv_disrupt Same as plink --cnv-disrupt
#' @param cnv_drop_no_segment Same as plink --cnv-drop-no-segment
#' @param cnv_dup Same as plink --cnv-dup
#' @param cnv_enrichment_test Same as plink --cnv-enrichment-test
#' @param cnv_exclude Same as plink --cnv-exclude
#' @param cnv_exclude_off_by_1 Same as plink --cnv-exclude-off-by-1
#' @param cnv_freq_excldue_above Same as plink --cnv-freq-excldue-above
#' @param cnv_freq_excldue_below Same as plink --cnv-freq-excldue-below
#' @param cnv_freq_excldue_exact Same as plink --cnv-freq-excldue-exact
#' @param cnv_freq_exclude_above Same as plink --cnv-freq-exclude-above
#' @param cnv_freq_exclude_below Same as plink --cnv-freq-exclude-below
#' @param cnv_freq_exclude_exact Same as plink --cnv-freq-exclude-exact
#' @param cnv_freq_incldue_exact Same as plink --cnv-freq-incldue-exact
#' @param cnv_freq_include_exact Same as plink --cnv-freq-include-exact
#' @param cnv_freq_method2 Same as plink --cnv-freq-method2
#' @param cnv_freq_overlap Same as plink --cnv-freq-overlap
#' @param cnv_green Same as plink --cnv-green
#' @param cnv_indiv_perm Same as plink --cnv-indiv-perm
#' @param cnv_intersect Same as plink --cnv-intersect
#' @param cnv_kb Same as plink --cnv-kb
#' @param cnv_list Same as plink --cnv-list
#' @param cnv_make_map Same as plink --cnv-make-map
#' @param cnv_max_kb Same as plink --cnv-max-kb
#' @param cnv_max_score Same as plink --cnv-max-score
#' @param cnv_max_sites Same as plink --cnv-max-sites
#' @param cnv_overlap Same as plink --cnv-overlap
#' @param cnv_red Same as plink --cnv-red
#' @param cnv_region_overlap Same as plink --cnv-region-overlap
#' @param cnv_report_regions Same as plink --cnv-report-regions
#' @param cnv_score Same as plink --cnv-score
#' @param cnv_seglist Same as plink --cnv-seglist
#' @param cnv_sites Same as plink --cnv-sites
#' @param cnv_subset Same as plink --cnv-subset
#' @param cnv_test Same as plink --cnv-test
#' @param cnv_test_1sided Same as plink --cnv-test-1sided
#' @param cnv_test_2sided Same as plink --cnv-test-2sided
#' @param cnv_test_region Same as plink --cnv-test-region
#' @param cnv_test_window Same as plink --cnv-test-window
#' @param cnv_track Same as plink --cnv-track
#' @param cnv_union_overlap Same as plink --cnv-union-overlap
#' @param cnv_unique Same as plink --cnv-unique
#' @param cnv_verbose_report_regions Same as plink --cnv-verbose-report-regions
#' @param cnv_write Same as plink --cnv-write
#' @param cnv_write_freq Same as plink --cnv-write-freq
#' @param complement_sets Same as plink --complement-sets
#' @param compound_genotypes Same as plink --compound-genotypes
#' @param compress Same as plink --compress
#' @param condition Same as plink --condition
#' @param condition_list Same as plink --condition-list
#' @param consensus_match Same as plink --consensus-match
#' @param const_fid Same as plink --const-fid
#' @param control Same as plink --control
#' @param counts Same as plink --counts
#' @param covar Same as plink --covar
#' @param covar_name Same as plink --covar-name
#' @param covar_number Same as plink --covar-number
#' @param cow Same as plink --cow
#' @param d Same as plink --d
#' @param data Same as plink --data
#' @param debug Same as plink --debug
#' @param decompress Same as plink --decompress
#' @param dfam Same as plink --dfam
#' @param distance Same as plink --distance
#' @param distance_exp Same as plink --distance-exp
#' @param distance_matrix Same as plink --distance-matrix
#' @param dog Same as plink --dog
#' @param dominant Same as plink --dominant
#' @param dosage Same as plink --dosage
#' @param double_id Same as plink --double-id
#' @param dprime Same as plink --dprime
#' @param dummy Same as plink --dummy
#' @param dummy_coding Same as plink --dummy-coding
#' @param each_versus_others Same as plink --each-versus-others
#' @param each_vs_others Same as plink --each-vs-others
#' @param epistasis Same as plink --epistasis
#' @param epistasis_summary_merge Same as plink --epistasis-summary-merge
#' @param exclude Same as plink --exclude
#' @param exclude_before_extract Same as plink --exclude-before-extract
#' @param exclude_snp Same as plink --exclude-snp
#' @param exclude_snps Same as plink --exclude-snps
#' @param extract Same as plink --extract
#' @param fam Same as plink --fam
#' @param family Same as plink --family
#' @param fast_epistasis Same as plink --fast-epistasis
#' @param fid Same as plink --fid
#' @param file Same as plink --file
#' @param fill_missing_a2 Same as plink --fill-missing-a2
#' @param filter Same as plink --filter
#' @param filter_cases Same as plink --filter-cases
#' @param filter_controls Same as plink --filter-controls
#' @param filter_females Same as plink --filter-females
#' @param filter_founders Same as plink --filter-founders
#' @param filter_males Same as plink --filter-males
#' @param filter_nonfounders Same as plink --filter-nonfounders
#' @param fisher Same as plink --fisher
#' @param flip Same as plink --flip
#' @param flip_scan Same as plink --flip-scan
#' @param flip_scan_threshold Same as plink --flip-scan-threshold
#' @param flip_scan_verbose Same as plink --flip-scan-verbose
#' @param flip_scan_window Same as plink --flip-scan-window
#' @param flip_scan_window_kb Same as plink --flip-scan-window-kb
#' @param flip_subset Same as plink --flip-subset
#' @param freq Same as plink --freq
#' @param freqx Same as plink --freqx
#' @param from Same as plink --from
#' @param from_bp Same as plink --from-bp
#' @param from_kb Same as plink --from-kb
#' @param from_mb Same as plink --from-mb
#' @param frqx Same as plink --frqx
#' @param fst Same as plink --fst
#' @param gap Same as plink --gap
#' @param gates Same as plink --gates
#' @param gc Same as plink --gc
#' @param gen Same as plink --gen
#' @param gene Same as plink --gene
#' @param gene_all Same as plink --gene-all
#' @param gene_list Same as plink --gene-list
#' @param gene_list_border Same as plink --gene-list-border
#' @param gene_report Same as plink --gene-report
#' @param gene_report_empty Same as plink --gene-report-empty
#' @param gene_report_snp_field Same as plink --gene-report-snp-field
#' @param gene_subset Same as plink --gene-subset
#' @param genedrop Same as plink --genedrop
#' @param genepi Same as plink --genepi
#' @param geno Same as plink --geno
#' @param genome Same as plink --genome
#' @param genome_full Same as plink --genome-full
#' @param genome_lists Same as plink --genome-lists
#' @param genome_minimal Same as plink --genome-minimal
#' @param genotypic Same as plink --genotypic
#' @param gfile Same as plink --gfile
#' @param gplink Same as plink --gplink
#' @param grm Same as plink --grm
#' @param grm_bin Same as plink --grm-bin
#' @param grm_gz Same as plink --grm-gz
#' @param group_avg Same as plink --group-avg
#' @param groupdist Same as plink --groupdist
#' @param gxe Same as plink --gxe
#' @param hap... Same as plink --hap...
#' @param hap Same as plink --hap
#' @param hap_assoc Same as plink --hap-assoc
#' @param hap_freq Same as plink --hap-freq
#' @param hap_impute Same as plink --hap-impute
#' @param hap_max_phase Same as plink --hap-max-phase
#' @param hap_min_phase_prob Same as plink --hap-min-phase-prob
#' @param hap_miss Same as plink --hap-miss
#' @param hap_phase Same as plink --hap-phase
#' @param hap_phase_wide Same as plink --hap-phase-wide
#' @param hap_pp Same as plink --hap-pp
#' @param hap_snps Same as plink --hap-snps
#' @param hap_tdt Same as plink --hap-tdt
#' @param hap_window Same as plink --hap-window
#' @param hard_call_threshold Same as plink --hard-call-threshold
#' @param hardy2 Same as plink --hardy2
#' @param hardy Same as plink --hardy
#' @param help Same as plink --help
#' @param het Same as plink --het
#' @param hethom Same as plink --hethom
#' @param hide_covar Same as plink --hide-covar
#' @param homog Same as plink --homog
#' @param homozyg Same as plink --homozyg
#' @param homozyg_density Same as plink --homozyg-density
#' @param homozyg_gap Same as plink --homozyg-gap
#' @param homozyg_group Same as plink --homozyg-group
#' @param homozyg_het Same as plink --homozyg-het
#' @param homozyg_include_missing Same as plink --homozyg-include-missing
#' @param homozyg_kb Same as plink --homozyg-kb
#' @param homozyg_match Same as plink --homozyg-match
#' @param homozyg_snp Same as plink --homozyg-snp
#' @param homozyg_verbose Same as plink --homozyg-verbose
#' @param homozyg_window_het Same as plink --homozyg-window-het
#' @param homozyg_window_kb Same as plink --homozyg-window-kb
#' @param homozyg_window_missing Same as plink --homozyg-window-missing
#' @param homozyg_window_snp Same as plink --homozyg-window-snp
#' @param homozyg_window_threshold Same as plink --homozyg-window-threshold
#' @param horse Same as plink --horse
#' @param hwe Same as plink --hwe
#' @param hwe_all Same as plink --hwe-all
#' @param ibc Same as plink --ibc
#' @param ibm Same as plink --ibm
#' @param ibs_matrix Same as plink --ibs-matrix
#' @param ibs_test Same as plink --ibs-test
#' @param id_delim Same as plink --id-delim
#' @param id_dict Same as plink --id-dict
#' @param id_match Same as plink --id-match
#' @param iid Same as plink --iid
#' @param impossible Same as plink --impossible
#' @param impute_sex Same as plink --impute-sex
#' @param ind_major Same as plink --ind-major
#' @param indep Same as plink --indep
#' @param indep_pairphase Same as plink --indep-pairphase
#' @param indep_pairwise Same as plink --indep-pairwise
#' @param independent_effect Same as plink --independent-effect
#' @param indiv_sort Same as plink --indiv-sort
#' @param inter_chr Same as plink --inter-chr
#' @param interaction Same as plink --interaction
#' @param je_cellmin Same as plink --je-cellmin
#' @param keep Same as plink --keep
#' @param keep_allele_order Same as plink --keep-allele-order
#' @param keep_autoconv Same as plink --keep-autoconv
#' @param keep_before_remove Same as plink --keep-before-remove
#' @param keep_cluster_names Same as plink --keep-cluster-names
#' @param keep_clusters Same as plink --keep-clusters
#' @param keep_fam Same as plink --keep-fam
#' @param lambda Same as plink --lambda
#' @param lasso Same as plink --lasso
#' @param lasso_select_covars Same as plink --lasso-select-covars
#' @param ld Same as plink --ld
#' @param ld_snp Same as plink --ld-snp
#' @param ld_snp_list Same as plink --ld-snp-list
#' @param ld_snps Same as plink --ld-snps
#' @param ld_window Same as plink --ld-window
#' @param ld_window_kb Same as plink --ld-window-kb
#' @param ld_window_r2 Same as plink --ld-window-r2
#' @param ld_xchr Same as plink --ld-xchr
#' @param lfile Same as plink --lfile
#' @param liability Same as plink --liability
#' @param linear Same as plink --linear
#' @param list Same as plink --list
#' @param list_23_indels Same as plink --list-23-indels
#' @param list_all Same as plink --list-all
#' @param logistic Same as plink --logistic
#' @param lookup... Same as plink --lookup...
#' @param lookup Same as plink --lookup
#' @param lookup_gene Same as plink --lookup-gene
#' @param lookup_list Same as plink --lookup-list
#' @param loop_assoc Same as plink --loop-assoc
#' @param maf Same as plink --maf
#' @param maf_succ Same as plink --maf-succ
#' @param make_bed Same as plink --make-bed
#' @param make_founders Same as plink --make-founders
#' @param make_grm Same as plink --make-grm
#' @param make_grm_bin Same as plink --make-grm-bin
#' @param make_grm_gz Same as plink --make-grm-gz
#' @param make_just_bim Same as plink --make-just-bim
#' @param make_just_fam Same as plink --make-just-fam
#' @param make_perm_pheno Same as plink --make-perm-pheno
#' @param make_pheno Same as plink --make-pheno
#' @param make_rel Same as plink --make-rel
#' @param make_set Same as plink --make-set
#' @param make_set_border Same as plink --make-set-border
#' @param make_set_collapse_group Same as plink --make-set-collapse-group
#' @param make_set_complement_all Same as plink --make-set-complement-all
#' @param make_set_complement_group Same as plink --make-set-complement-group
#' @param map Same as plink --map
#' @param mat Same as plink --mat
#' @param match Same as plink --match
#' @param match_type Same as plink --match-type
#' @param matrix Same as plink --matrix
#' @param max Same as plink --max
#' @param max_maf Same as plink --max-maf
#' @param mc Same as plink --mc
#' @param mcc Same as plink --mcc
#' @param mcovar Same as plink --mcovar
#' @param mds_cluster Same as plink --mds-cluster
#' @param mds_plot Same as plink --mds-plot
#' @param me Same as plink --me
#' @param me_exclude_one Same as plink --me-exclude-one
#' @param memory Same as plink --memory
#' @param mendel Same as plink --mendel
#' @param mendel_duos Same as plink --mendel-duos
#' @param mendel_multigen Same as plink --mendel-multigen
#' @param merge Same as plink --merge
#' @param merge_equal_pos Same as plink --merge-equal-pos
#' @param merge_list Same as plink --merge-list
#' @param merge_mode Same as plink --merge-mode
#' @param merge_x Same as plink --merge-x
#' @param meta_analysis Same as plink --meta-analysis
#' @param meta_analysis_..._field Same as plink --meta-analysis-...-field
#' @param mfilter Same as plink --mfilter
#' @param mh Same as plink --mh
#' @param mhf Same as plink --mhf
#' @param min Same as plink --min
#' @param mind Same as plink --mind
#' @param mishap_window Same as plink --mishap-window
#' @param missing Same as plink --missing
#' @param missing_code Same as plink --missing-code
#' @param missing_genotype Same as plink --missing-genotype
#' @param missing_phenotype Same as plink --missing-phenotype
#' @param missing_var_code Same as plink --missing-var-code
#' @param mlma Same as plink --mlma
#' @param mlma_loco Same as plink --mlma-loco
#' @param mlma_no_adj_covar Same as plink --mlma-no-adj-covar
#' @param model Same as plink --model
#' @param model_dom Same as plink --model-dom
#' @param model_gen Same as plink --model-gen
#' @param model_rec Same as plink --model-rec
#' @param model_trend Same as plink --model-trend
#' @param mouse Same as plink --mouse
#' @param mperm Same as plink --mperm
#' @param mperm_save Same as plink --mperm-save
#' @param mperm_save_all Same as plink --mperm-save-all
#' @param mpheno Same as plink --mpheno
#' @param must_have_sex Same as plink --must-have-sex
#' @param mwithin Same as plink --mwithin
#' @param neighbour Same as plink --neighbour
#' @param no_fid Same as plink --no-fid
#' @param no_parents Same as plink --no-parents
#' @param no_pheno Same as plink --no-pheno
#' @param no_sex Same as plink --no-sex
#' @param no_snp Same as plink --no-snp
#' @param no_x_sex Same as plink --no-x-sex
#' @param nonfounders Same as plink --nonfounders
#' @param nop Same as plink --nop
#' @param not_chr Same as plink --not-chr
#' @param nudge Same as plink --nudge
#' @param null_group Same as plink --null-group
#' @param null_snp Same as plink --null-snp
#' @param oblig_cluster Same as plink --oblig-cluster
#' @param oblig_clusters Same as plink --oblig-clusters
#' @param oblig_missing Same as plink --oblig-missing
#' @param out Same as plink --out
#' @param output_chr Same as plink --output-chr
#' @param output_missing_genotype Same as plink --output-missing-genotype
#' @param output_missing_phenotype Same as plink --output-missing-phenotype
#' @param oxford_pheno_name Same as plink --oxford-pheno-name
#' @param parallel Same as plink --parallel
#' @param parameters Same as plink --parameters
#' @param parentdt1 Same as plink --parentdt1
#' @param parentdt2 Same as plink --parentdt2
#' @param pat Same as plink --pat
#' @param pca Same as plink --pca
#' @param pca_cluster_names Same as plink --pca-cluster-names
#' @param pca_clusters Same as plink --pca-clusters
#' @param ped Same as plink --ped
#' @param pedigree Same as plink --pedigree
#' @param perm Same as plink --perm
#' @param perm_batch_size Same as plink --perm-batch-size
#' @param perm_count Same as plink --perm-count
#' @param pfilter Same as plink --pfilter
#' @param pheno Same as plink --pheno
#' @param pheno_merge Same as plink --pheno-merge
#' @param pheno_name Same as plink --pheno-name
#' @param pick1 Same as plink --pick1
#' @param plist Same as plink --plist
#' @param poo Same as plink --poo
#' @param pool_size Same as plink --pool-size
#' @param ppc Same as plink --ppc
#' @param ppc_gap Same as plink --ppc-gap
#' @param proxy_... Same as plink --proxy-...
#' @param proxy_assoc Same as plink --proxy-assoc
#' @param proxy_b_kb Same as plink --proxy-b-kb
#' @param proxy_b_maxsnp Same as plink --proxy-b-maxsnp
#' @param proxy_b_r2 Same as plink --proxy-b-r2
#' @param proxy_b_threshold Same as plink --proxy-b-threshold
#' @param proxy_b_window Same as plink --proxy-b-window
#' @param proxy_dosage Same as plink --proxy-dosage
#' @param proxy_drop Same as plink --proxy-drop
#' @param proxy_flanking Same as plink --proxy-flanking
#' @param proxy_geno Same as plink --proxy-geno
#' @param proxy_genotypic_concordance Same as plink --proxy-genotypic-concordance
#' @param proxy_glm Same as plink --proxy-glm
#' @param proxy_impute Same as plink --proxy-impute
#' @param proxy_impute_threshold Same as plink --proxy-impute-threshold
#' @param proxy_kb Same as plink --proxy-kb
#' @param proxy_list Same as plink --proxy-list
#' @param proxy_maf Same as plink --proxy-maf
#' @param proxy_maxsnp Same as plink --proxy-maxsnp
#' @param proxy_mhf Same as plink --proxy-mhf
#' @param proxy_r2 Same as plink --proxy-r2
#' @param proxy_r2_no_filter Same as plink --proxy-r2-no-filter
#' @param proxy_replace Same as plink --proxy-replace
#' @param proxy_show_proxies Same as plink --proxy-show-proxies
#' @param proxy_sub_maxsnp Same as plink --proxy-sub-maxsnp
#' @param proxy_sub_r2 Same as plink --proxy-sub-r2
#' @param proxy_tdt Same as plink --proxy-tdt
#' @param proxy_verbose Same as plink --proxy-verbose
#' @param proxy_window Same as plink --proxy-window
#' @param prune Same as plink --prune
#' @param q_score_file Same as plink --q-score-file
#' @param q_score_range Same as plink --q-score-range
#' @param qfam... Same as plink --qfam...
#' @param qmatch Same as plink --qmatch
#' @param qq_plot Same as plink --qq-plot
#' @param qt Same as plink --qt
#' @param qt_means Same as plink --qt-means
#' @param qual_geno_... Same as plink --qual-geno-...
#' @param qual_geno_max_threshold Same as plink --qual-geno-max-threshold
#' @param qual_geno_scores Same as plink --qual-geno-scores
#' @param qual_geno_threshold Same as plink --qual-geno-threshold
#' @param qual_max_threshold Same as plink --qual-max-threshold
#' @param qual_scores Same as plink --qual-scores
#' @param qual_threshold Same as plink --qual-threshold
#' @param r2 Same as plink --r2
#' @param r Same as plink --r
#' @param range Same as plink --range
#' @param rank Same as plink --rank
#' @param read_dists Same as plink --read-dists
#' @param read_freq Same as plink --read-freq
#' @param read_genome Same as plink --read-genome
#' @param read_genome_list Same as plink --read-genome-list
#' @param read_genome_minimal Same as plink --read-genome-minimal
#' @param recessive Same as plink --recessive
#' @param recode12 Same as plink --recode12
#' @param recode Same as plink --recode
#' @param recodeA Same as plink --recodeA
#' @param recodeAD Same as plink --recodeAD
#' @param recodeHV Same as plink --recodeHV
#' @param recode_allele Same as plink --recode-allele
#' @param recode_beagle Same as plink --recode-beagle
#' @param recode_bimbam Same as plink --recode-bimbam
#' @param recode_fastphase Same as plink --recode-fastphase
#' @param recode_lgen Same as plink --recode-lgen
#' @param recode_rlist Same as plink --recode-rlist
#' @param recode_structure Same as plink --recode-structure
#' @param recode_vcf Same as plink --recode-vcf
#' @param recode_whap Same as plink --recode-whap
#' @param reference Same as plink --reference
#' @param reference_allele Same as plink --reference-allele
#' @param regress_distance Same as plink --regress-distance
#' @param regress_pcs Same as plink --regress-pcs
#' @param regress_rel Same as plink --regress-rel
#' @param rel_check Same as plink --rel-check
#' @param rel_cutoff Same as plink --rel-cutoff
#' @param remove Same as plink --remove
#' @param remove_cluster_names Same as plink --remove-cluster-names
#' @param remove_clusters Same as plink --remove-clusters
#' @param remove_fam Same as plink --remove-fam
#' @param rerun Same as plink --rerun
#' @param rice Same as plink --rice
#' @param sample Same as plink --sample
#' @param score Same as plink --score
#' @param score_no_mean_imputation Same as plink --score-no-mean-imputation
#' @param script Same as plink --script
#' @param seed Same as plink --seed
#' @param set Same as plink --set
#' @param set_by_all Same as plink --set-by-all
#' @param set_collapse_all Same as plink --set-collapse-all
#' @param set_hh_missing Same as plink --set-hh-missing
#' @param set_max Same as plink --set-max
#' @param set_me_missing Same as plink --set-me-missing
#' @param set_missing_nonsnp_ids Same as plink --set-missing-nonsnp-ids
#' @param set_missing_snp_ids Same as plink --set-missing-snp-ids
#' @param set_missing_var_ids Same as plink --set-missing-var-ids
#' @param set_names Same as plink --set-names
#' @param set_p Same as plink --set-p
#' @param set_r2 Same as plink --set-r2
#' @param set_r2_phase Same as plink --set-r2-phase
#' @param set_table Same as plink --set-table
#' @param set_test Same as plink --set-test
#' @param sex Same as plink --sex
#' @param sheep Same as plink --sheep
#' @param show_tags Same as plink --show-tags
#' @param silent Same as plink --silent
#' @param simulate Same as plink --simulate
#' @param simulate_haps Same as plink --simulate-haps
#' @param simulate_label Same as plink --simulate-label
#' @param simulate_missing Same as plink --simulate-missing
#' @param simulate_n Same as plink --simulate-n
#' @param simulate_ncases Same as plink --simulate-ncases
#' @param simulate_ncontrols Same as plink --simulate-ncontrols
#' @param simulate_prevalence Same as plink --simulate-prevalence
#' @param simulate_qt Same as plink --simulate-qt
#' @param simulate_tags Same as plink --simulate-tags
#' @param snp Same as plink --snp
#' @param snps Same as plink --snps
#' @param snps_only Same as plink --snps-only
#' @param specific_haplotype Same as plink --specific-haplotype
#' @param split_x Same as plink --split-x
#' @param standard_beta Same as plink --standard-beta
#' @param subset Same as plink --subset
#' @param swap_parents Same as plink --swap-parents
#' @param swap_sibs Same as plink --swap-sibs
#' @param swap_unrel Same as plink --swap-unrel
#' @param tab Same as plink --tab
#' @param tag_kb Same as plink --tag-kb
#' @param tag_mode2 Same as plink --tag-mode2
#' @param tag_r2 Same as plink --tag-r2
#' @param tail_pheno Same as plink --tail-pheno
#' @param tdt Same as plink --tdt
#' @param test_all Same as plink --test-all
#' @param test_mishap Same as plink --test-mishap
#' @param test_missing Same as plink --test-missing
#' @param test_snp Same as plink --test-snp
#' @param tests Same as plink --tests
#' @param tfam Same as plink --tfam
#' @param tfile Same as plink --tfile
#' @param thin Same as plink --thin
#' @param thin_count Same as plink --thin-count
#' @param threads Same as plink --threads
#' @param to Same as plink --to
#' @param to_bp Same as plink --to-bp
#' @param to_kb Same as plink --to-kb
#' @param to_mb Same as plink --to-mb
#' @param tped Same as plink --tped
#' @param transpose Same as plink --transpose
#' @param trend Same as plink --trend
#' @param tucc Same as plink --tucc
#' @param twolocus Same as plink --twolocus
#' @param unbounded Same as plink --unbounded
#' @param unrelated_heritability Same as plink --unrelated-heritability
#' @param update_alleles Same as plink --update-alleles
#' @param update_chr Same as plink --update-chr
#' @param update_cm Same as plink --update-cm
#' @param update_ids Same as plink --update-ids
#' @param update_map Same as plink --update-map
#' @param update_name Same as plink --update-name
#' @param update_parents Same as plink --update-parents
#' @param update_sex Same as plink --update-sex
#' @param vcf Same as plink --vcf
#' @param vcf_filter Same as plink --vcf-filter
#' @param vcf_half_call Same as plink --vcf-half-call
#' @param vcf_idspace_to Same as plink --vcf-idspace-to
#' @param vcf_min_qual Same as plink --vcf-min-qual
#' @param vegas Same as plink --vegas
#' @param version Same as plink --version
#' @param vif Same as plink --vif
#' @param whap Same as plink --whap
#' @param window Same as plink --window
#' @param with_freqs Same as plink --with-freqs
#' @param with_phenotype Same as plink --with-phenotype
#' @param with_reference Same as plink --with-reference
#' @param within Same as plink --within
#' @param write_cluster Same as plink --write-cluster
#' @param write_covar Same as plink --write-covar
#' @param write_dosage Same as plink --write-dosage
#' @param write_set Same as plink --write-set
#' @param write_set_r2 Same as plink --write-set-r2
#' @param write_snplist Same as plink --write-snplist
#' @param xchr_model Same as plink --xchr-model
#' @param zero_cluster Same as plink --zero-cluster
#' @param zero_cms Same as plink --zero-cms
#' @param one Same as plink --1
#' @param twothreefile Same as plink --23file
#' @param wait Logical. If FALSE, the plink process will fork into the background.
#' @param stdout Passed to system2, see its documentation.
#' @param stderr Passed to system2, see its documentation.
#' @param plinkcollFileStems A character vector of all bed file stems you want to pass to plink.
getPlinkParam = function(
D=NULL,
K=NULL,
a1_allele=NULL,
a2_allele=NULL,
adjust=NULL,
all=NULL,
all_pheno=NULL,
allele1234=NULL,
alleleACGT=NULL,
allele_count=NULL,
allow_extra_chr=NULL,
allow_no_sex=NULL,
alt_group=NULL,
alt_snp=NULL,
annotate=NULL,
annotate_snp_field=NULL,
aperm=NULL,
assoc=NULL,
attrib=NULL,
attrib_indiv=NULL,
autosome=NULL,
autosome_num=NULL,
autosome_xy=NULL,
bcf=NULL,
bd=NULL,
bed=NULL,
beta=NULL,
bfile=NULL,
bgen=NULL,
biallelic_only=NULL,
bim=NULL,
blocks=NULL,
blocks_inform_frac=NULL,
blocks_max_kb=NULL,
blocks_min_maf=NULL,
blocks_recomb_highci=NULL,
blocks_strong_highci=NULL,
blocks_strong_lowci=NULL,
bmerge=NULL,
border=NULL,
bp_space=NULL,
case_only=NULL,
cc=NULL,
cell=NULL,
cfile=NULL,
chap=NULL,
check_sex=NULL,
chr=NULL,
chr_set=NULL,
ci=NULL,
clump=NULL,
clump_allow_overlap=NULL,
clump_annotate=NULL,
clump_best=NULL,
clump_field=NULL,
clump_index_first=NULL,
clump_kb=NULL,
clump_p1=NULL,
clump_p2=NULL,
clump_r2=NULL,
clump_range=NULL,
clump_range_border=NULL,
clump_replicate=NULL,
clump_snp_field=NULL,
clump_verbose=NULL,
cluster=NULL,
cluster_missing=NULL,
cm_map=NULL,
cnv_blue=NULL,
cnv_border=NULL,
cnv_brown=NULL,
cnv_check_no_overlap=NULL,
cnv_count=NULL,
cnv_del=NULL,
cnv_disrupt=NULL,
cnv_drop_no_segment=NULL,
cnv_dup=NULL,
cnv_enrichment_test=NULL,
cnv_exclude=NULL,
cnv_exclude_off_by_1=NULL,
cnv_freq_excldue_above=NULL,
cnv_freq_excldue_below=NULL,
cnv_freq_excldue_exact=NULL,
cnv_freq_exclude_above=NULL,
cnv_freq_exclude_below=NULL,
cnv_freq_exclude_exact=NULL,
cnv_freq_incldue_exact=NULL,
cnv_freq_include_exact=NULL,
cnv_freq_method2=NULL,
cnv_freq_overlap=NULL,
cnv_green=NULL,
cnv_indiv_perm=NULL,
cnv_intersect=NULL,
cnv_kb=NULL,
cnv_list=NULL,
cnv_make_map=NULL,
cnv_max_kb=NULL,
cnv_max_score=NULL,
cnv_max_sites=NULL,
cnv_overlap=NULL,
cnv_red=NULL,
cnv_region_overlap=NULL,
cnv_report_regions=NULL,
cnv_score=NULL,
cnv_seglist=NULL,
cnv_sites=NULL,
cnv_subset=NULL,
cnv_test=NULL,
cnv_test_1sided=NULL,
cnv_test_2sided=NULL,
cnv_test_region=NULL,
cnv_test_window=NULL,
cnv_track=NULL,
cnv_union_overlap=NULL,
cnv_unique=NULL,
cnv_verbose_report_regions=NULL,
cnv_write=NULL,
cnv_write_freq=NULL,
complement_sets=NULL,
compound_genotypes=NULL,
compress=NULL,
condition=NULL,
condition_list=NULL,
consensus_match=NULL,
const_fid=NULL,
control=NULL,
counts=NULL,
covar=NULL,
covar_name=NULL,
covar_number=NULL,
cow=NULL,
d=NULL,
data=NULL,
debug=NULL,
decompress=NULL,
dfam=NULL,
distance=NULL,
distance_exp=NULL,
distance_matrix=NULL,
dog=NULL,
dominant=NULL,
dosage=NULL,
double_id=NULL,
dprime=NULL,
dummy=NULL,
dummy_coding=NULL,
each_versus_others=NULL,
each_vs_others=NULL,
epistasis=NULL,
epistasis_summary_merge=NULL,
exclude=NULL,
exclude_before_extract=NULL,
exclude_snp=NULL,
exclude_snps=NULL,
extract=NULL,
fam=NULL,
family=NULL,
fast_epistasis=NULL,
fid=NULL,
file=NULL,
fill_missing_a2=NULL,
filter=NULL,
filter_cases=NULL,
filter_controls=NULL,
filter_females=NULL,
filter_founders=NULL,
filter_males=NULL,
filter_nonfounders=NULL,
fisher=NULL,
flip=NULL,
flip_scan=NULL,
flip_scan_threshold=NULL,
flip_scan_verbose=NULL,
flip_scan_window=NULL,
flip_scan_window_kb=NULL,
flip_subset=NULL,
freq=NULL,
freqx=NULL,
from=NULL,
from_bp=NULL,
from_kb=NULL,
from_mb=NULL,
frqx=NULL,
fst=NULL,
gap=NULL,
gates=NULL,
gc=NULL,
gen=NULL,
gene=NULL,
gene_all=NULL,
gene_list=NULL,
gene_list_border=NULL,
gene_report=NULL,
gene_report_empty=NULL,
gene_report_snp_field=NULL,
gene_subset=NULL,
genedrop=NULL,
genepi=NULL,
geno=NULL,
genome=NULL,
genome_full=NULL,
genome_lists=NULL,
genome_minimal=NULL,
genotypic=NULL,
gfile=NULL,
gplink=NULL,
grm=NULL,
grm_bin=NULL,
grm_gz=NULL,
group_avg=NULL,
groupdist=NULL,
gxe=NULL,
hap...=NULL,
hap=NULL,
hap_assoc=NULL,
hap_freq=NULL,
hap_impute=NULL,
hap_max_phase=NULL,
hap_min_phase_prob=NULL,
hap_miss=NULL,
hap_phase=NULL,
hap_phase_wide=NULL,
hap_pp=NULL,
hap_snps=NULL,
hap_tdt=NULL,
hap_window=NULL,
hard_call_threshold=NULL,
hardy2=NULL,
hardy=NULL,
help=NULL,
het=NULL,
hethom=NULL,
hide_covar=NULL,
homog=NULL,
homozyg=NULL,
homozyg_density=NULL,
homozyg_gap=NULL,
homozyg_group=NULL,
homozyg_het=NULL,
homozyg_include_missing=NULL,
homozyg_kb=NULL,
homozyg_match=NULL,
homozyg_snp=NULL,
homozyg_verbose=NULL,
homozyg_window_het=NULL,
homozyg_window_kb=NULL,
homozyg_window_missing=NULL,
homozyg_window_snp=NULL,
homozyg_window_threshold=NULL,
horse=NULL,
hwe=NULL,
hwe_all=NULL,
ibc=NULL,
ibm=NULL,
ibs_matrix=NULL,
ibs_test=NULL,
id_delim=NULL,
id_dict=NULL,
id_match=NULL,
iid=NULL,
impossible=NULL,
impute_sex=NULL,
ind_major=NULL,
indep=NULL,
indep_pairphase=NULL,
indep_pairwise=NULL,
independent_effect=NULL,
indiv_sort=NULL,
inter_chr=NULL,
interaction=NULL,
je_cellmin=NULL,
keep=NULL,
keep_allele_order=NULL,
keep_autoconv=NULL,
keep_before_remove=NULL,
keep_cluster_names=NULL,
keep_clusters=NULL,
keep_fam=NULL,
lambda=NULL,
lasso=NULL,
lasso_select_covars=NULL,
ld=NULL,
ld_snp=NULL,
ld_snp_list=NULL,
ld_snps=NULL,
ld_window=NULL,
ld_window_kb=NULL,
ld_window_r2=NULL,
ld_xchr=NULL,
lfile=NULL,
liability=NULL,
linear=NULL,
list=NULL,
list_23_indels=NULL,
list_all=NULL,
logistic=NULL,
lookup...=NULL,
lookup=NULL,
lookup_gene=NULL,
lookup_list=NULL,
loop_assoc=NULL,
maf=NULL,
maf_succ=NULL,
make_bed=NULL,
make_founders=NULL,
make_grm=NULL,
make_grm_bin=NULL,
make_grm_gz=NULL,
make_just_bim=NULL,
make_just_fam=NULL,
make_perm_pheno=NULL,
make_pheno=NULL,
make_rel=NULL,
make_set=NULL,
make_set_border=NULL,
make_set_collapse_group=NULL,
make_set_complement_all=NULL,
make_set_complement_group=NULL,
map=NULL,
mat=NULL,
match=NULL,
match_type=NULL,
matrix=NULL,
max=NULL,
max_maf=NULL,
mc=NULL,
mcc=NULL,
mcovar=NULL,
mds_cluster=NULL,
mds_plot=NULL,
me=NULL,
me_exclude_one=NULL,
memory=NULL,
mendel=NULL,
mendel_duos=NULL,
mendel_multigen=NULL,
merge=NULL,
merge_equal_pos=NULL,
merge_list=NULL,
merge_mode=NULL,
merge_x=NULL,
meta_analysis=NULL,
meta_analysis_..._field=NULL,
mfilter=NULL,
mh=NULL,
mhf=NULL,
min=NULL,
mind=NULL,
mishap_window=NULL,
missing=NULL,
missing_code=NULL,
missing_genotype=NULL,
missing_phenotype=NULL,
missing_var_code=NULL,
mlma=NULL,
mlma_loco=NULL,
mlma_no_adj_covar=NULL,
model=NULL,
model_dom=NULL,
model_gen=NULL,
model_rec=NULL,
model_trend=NULL,
mouse=NULL,
mperm=NULL,
mperm_save=NULL,
mperm_save_all=NULL,
mpheno=NULL,
must_have_sex=NULL,
mwithin=NULL,
neighbour=NULL,
no_fid=NULL,
no_parents=NULL,
no_pheno=NULL,
no_sex=NULL,
no_snp=NULL,
no_x_sex=NULL,
nonfounders=NULL,
nop=NULL,
not_chr=NULL,
nudge=NULL,
null_group=NULL,
null_snp=NULL,
oblig_cluster=NULL,
oblig_clusters=NULL,
oblig_missing=NULL,
out=NULL,
output_chr=NULL,
output_missing_genotype=NULL,
output_missing_phenotype=NULL,
oxford_pheno_name=NULL,
parallel=NULL,
parameters=NULL,
parentdt1=NULL,
parentdt2=NULL,
pat=NULL,
pca=NULL,
pca_cluster_names=NULL,
pca_clusters=NULL,
ped=NULL,
pedigree=NULL,
perm=NULL,
perm_batch_size=NULL,
perm_count=NULL,
pfilter=NULL,
pheno=NULL,
pheno_merge=NULL,
pheno_name=NULL,
pick1=NULL,
plist=NULL,
poo=NULL,
pool_size=NULL,
ppc=NULL,
ppc_gap=NULL,
proxy_...=NULL,
proxy_assoc=NULL,
proxy_b_kb=NULL,
proxy_b_maxsnp=NULL,
proxy_b_r2=NULL,
proxy_b_threshold=NULL,
proxy_b_window=NULL,
proxy_dosage=NULL,
proxy_drop=NULL,
proxy_flanking=NULL,
proxy_geno=NULL,
proxy_genotypic_concordance=NULL,
proxy_glm=NULL,
proxy_impute=NULL,
proxy_impute_threshold=NULL,
proxy_kb=NULL,
proxy_list=NULL,
proxy_maf=NULL,
proxy_maxsnp=NULL,
proxy_mhf=NULL,
proxy_r2=NULL,
proxy_r2_no_filter=NULL,
proxy_replace=NULL,
proxy_show_proxies=NULL,
proxy_sub_maxsnp=NULL,
proxy_sub_r2=NULL,
proxy_tdt=NULL,
proxy_verbose=NULL,
proxy_window=NULL,
prune=NULL,
q_score_file=NULL,
q_score_range=NULL,
qfam...=NULL,
qmatch=NULL,
qq_plot=NULL,
qt=NULL,
qt_means=NULL,
qual_geno_...=NULL,
qual_geno_max_threshold=NULL,
qual_geno_scores=NULL,
qual_geno_threshold=NULL,
qual_max_threshold=NULL,
qual_scores=NULL,
qual_threshold=NULL,
r2=NULL,
r=NULL,
range=NULL,
rank=NULL,
read_dists=NULL,
read_freq=NULL,
read_genome=NULL,
read_genome_list=NULL,
read_genome_minimal=NULL,
recessive=NULL,
recode12=NULL,
recode=NULL,
recodeA=NULL,
recodeAD=NULL,
recodeHV=NULL,
recode_allele=NULL,
recode_beagle=NULL,
recode_bimbam=NULL,
recode_fastphase=NULL,
recode_lgen=NULL,
recode_rlist=NULL,
recode_structure=NULL,
recode_vcf=NULL,
recode_whap=NULL,
reference=NULL,
reference_allele=NULL,
regress_distance=NULL,
regress_pcs=NULL,
regress_rel=NULL,
rel_check=NULL,
rel_cutoff=NULL,
remove=NULL,
remove_cluster_names=NULL,
remove_clusters=NULL,
remove_fam=NULL,
rerun=NULL,
rice=NULL,
sample=NULL,
score=NULL,
score_no_mean_imputation=NULL,
script=NULL,
seed=NULL,
set=NULL,
set_by_all=NULL,
set_collapse_all=NULL,
set_hh_missing=NULL,
set_max=NULL,
set_me_missing=NULL,
set_missing_nonsnp_ids=NULL,
set_missing_snp_ids=NULL,
set_missing_var_ids=NULL,
set_names=NULL,
set_p=NULL,
set_r2=NULL,
set_r2_phase=NULL,
set_table=NULL,
set_test=NULL,
sex=NULL,
sheep=NULL,
show_tags=NULL,
silent=NULL,
simulate=NULL,
simulate_haps=NULL,
simulate_label=NULL,
simulate_missing=NULL,
simulate_n=NULL,
simulate_ncases=NULL,
simulate_ncontrols=NULL,
simulate_prevalence=NULL,
simulate_qt=NULL,
simulate_tags=NULL,
snp=NULL,
snps=NULL,
snps_only=NULL,
specific_haplotype=NULL,
split_x=NULL,
standard_beta=NULL,
subset=NULL,
swap_parents=NULL,
swap_sibs=NULL,
swap_unrel=NULL,
tab=NULL,
tag_kb=NULL,
tag_mode2=NULL,
tag_r2=NULL,
tail_pheno=NULL,
tdt=NULL,
test_all=NULL,
test_mishap=NULL,
test_missing=NULL,
test_snp=NULL,
tests=NULL,
tfam=NULL,
tfile=NULL,
thin=NULL,
thin_count=NULL,
threads=NULL,
to=NULL,
to_bp=NULL,
to_kb=NULL,
to_mb=NULL,
tped=NULL,
transpose=NULL,
trend=NULL,
tucc=NULL,
twolocus=NULL,
unbounded=NULL,
unrelated_heritability=NULL,
update_alleles=NULL,
update_chr=NULL,
update_cm=NULL,
update_ids=NULL,
update_map=NULL,
update_name=NULL,
update_parents=NULL,
update_sex=NULL,
vcf=NULL,
vcf_filter=NULL,
vcf_half_call=NULL,
vcf_idspace_to=NULL,
vcf_min_qual=NULL,
vegas=NULL,
version=NULL,
vif=NULL,
whap=NULL,
window=NULL,
with_freqs=NULL,
with_phenotype=NULL,
with_reference=NULL,
within=NULL,
write_cluster=NULL,
write_covar=NULL,
write_dosage=NULL,
write_set=NULL,
write_set_r2=NULL,
write_snplist=NULL,
xchr_model=NULL,
zero_cluster=NULL,
zero_cms=NULL,
one = NULL,
twothreefile = NULL,
wait=TRUE,
stdout="",
stderr="",
plinkcollFileStems=NULL
) {
argList = as.list(match.call())[-1]
argList
}
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