getPlinkParam: Get a list of parameters for passing to plinkr
In kindlychung/CollapsABEL: An R package for quantitative CDH analysis
Description
Usage
Arguments
Details
View source: R/getPlinkParam.R
Description
Get a list of parameters for passing to plinkr
Usage
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getPlinkParam(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)
Arguments
D
Same as plink –D
K
Same as plink –K
a1_allele
Same as plink –a1-allele
a2_allele
Same as plink –a2-allele
adjust
Same as plink –adjust
all
Same as plink –all
all_pheno
Same as plink –all-pheno
allele1234
Same as plink –allele1234
alleleACGT
Same as plink –alleleACGT
allele_count
Same as plink –allele-count
allow_extra_chr
Same as plink –allow-extra-chr
allow_no_sex
Same as plink –allow-no-sex
alt_group
Same as plink –alt-group
alt_snp
Same as plink –alt-snp
annotate
Same as plink –annotate
annotate_snp_field
Same as plink –annotate-snp-field
aperm
Same as plink –aperm
assoc
Same as plink –assoc
attrib
Same as plink –attrib
attrib_indiv
Same as plink –attrib-indiv
autosome
Same as plink –autosome
autosome_num
Same as plink –autosome-num
autosome_xy
Same as plink –autosome-xy
bcf
Same as plink –bcf
bd
Same as plink –bd
bed
Same as plink –bed
beta
Same as plink –beta
bfile
Same as plink –bfile
bgen
Same as plink –bgen
biallelic_only
Same as plink –biallelic-only
bim
Same as plink –bim
blocks
Same as plink –blocks
blocks_inform_frac
Same as plink –blocks-inform-frac
blocks_max_kb
Same as plink –blocks-max-kb
blocks_min_maf
Same as plink –blocks-min-maf
blocks_recomb_highci
Same as plink –blocks-recomb-highci
blocks_strong_highci
Same as plink –blocks-strong-highci
blocks_strong_lowci
Same as plink –blocks-strong-lowci
bmerge
Same as plink –bmerge
border
Same as plink –border
bp_space
Same as plink –bp-space
case_only
Same as plink –case-only
cc
Same as plink –cc
cell
Same as plink –cell
cfile
Same as plink –cfile
chap
Same as plink –chap
check_sex
Same as plink –check-sex
chr
Same as plink –chr
chr_set
Same as plink –chr-set
ci
Same as plink –ci
clump
Same as plink –clump
clump_allow_overlap
Same as plink –clump-allow-overlap
clump_annotate
Same as plink –clump-annotate
clump_best
Same as plink –clump-best
clump_field
Same as plink –clump-field
clump_index_first
Same as plink –clump-index-first
clump_kb
Same as plink –clump-kb
clump_p1
Same as plink –clump-p1
clump_p2
Same as plink –clump-p2
clump_r2
Same as plink –clump-r2
clump_range
Same as plink –clump-range
clump_range_border
Same as plink –clump-range-border
clump_replicate
Same as plink –clump-replicate
clump_snp_field
Same as plink –clump-snp-field
clump_verbose
Same as plink –clump-verbose
cluster
Same as plink –cluster
cluster_missing
Same as plink –cluster-missing
cm_map
Same as plink –cm-map
cnv_blue
Same as plink –cnv-blue
cnv_border
Same as plink –cnv-border
cnv_brown
Same as plink –cnv-brown
cnv_check_no_overlap
Same as plink –cnv-check-no-overlap
cnv_count
Same as plink –cnv-count
cnv_del
Same as plink –cnv-del
cnv_disrupt
Same as plink –cnv-disrupt
cnv_drop_no_segment
Same as plink –cnv-drop-no-segment
cnv_dup
Same as plink –cnv-dup
cnv_enrichment_test
Same as plink –cnv-enrichment-test
cnv_exclude
Same as plink –cnv-exclude
cnv_exclude_off_by_1
Same as plink –cnv-exclude-off-by-1
cnv_freq_excldue_above
Same as plink –cnv-freq-excldue-above
cnv_freq_excldue_below
Same as plink –cnv-freq-excldue-below
cnv_freq_excldue_exact
Same as plink –cnv-freq-excldue-exact
cnv_freq_exclude_above
Same as plink –cnv-freq-exclude-above
cnv_freq_exclude_below
Same as plink –cnv-freq-exclude-below
cnv_freq_exclude_exact
Same as plink –cnv-freq-exclude-exact
cnv_freq_incldue_exact
Same as plink –cnv-freq-incldue-exact
cnv_freq_include_exact
Same as plink –cnv-freq-include-exact
cnv_freq_method2
Same as plink –cnv-freq-method2
cnv_freq_overlap
Same as plink –cnv-freq-overlap
cnv_green
Same as plink –cnv-green
cnv_indiv_perm
Same as plink –cnv-indiv-perm
cnv_intersect
Same as plink –cnv-intersect
cnv_kb
Same as plink –cnv-kb
cnv_list
Same as plink –cnv-list
cnv_make_map
Same as plink –cnv-make-map
cnv_max_kb
Same as plink –cnv-max-kb
cnv_max_score
Same as plink –cnv-max-score
cnv_max_sites
Same as plink –cnv-max-sites
cnv_overlap
Same as plink –cnv-overlap
cnv_red
Same as plink –cnv-red
cnv_region_overlap
Same as plink –cnv-region-overlap
cnv_report_regions
Same as plink –cnv-report-regions
cnv_score
Same as plink –cnv-score
cnv_seglist
Same as plink –cnv-seglist
cnv_sites
Same as plink –cnv-sites
cnv_subset
Same as plink –cnv-subset
cnv_test
Same as plink –cnv-test
cnv_test_1sided
Same as plink –cnv-test-1sided
cnv_test_2sided
Same as plink –cnv-test-2sided
cnv_test_region
Same as plink –cnv-test-region
cnv_test_window
Same as plink –cnv-test-window
cnv_track
Same as plink –cnv-track
cnv_union_overlap
Same as plink –cnv-union-overlap
cnv_unique
Same as plink –cnv-unique
cnv_verbose_report_regions
Same as plink –cnv-verbose-report-regions
cnv_write
Same as plink –cnv-write
cnv_write_freq
Same as plink –cnv-write-freq
complement_sets
Same as plink –complement-sets
compound_genotypes
Same as plink –compound-genotypes
compress
Same as plink –compress
condition
Same as plink –condition
condition_list
Same as plink –condition-list
consensus_match
Same as plink –consensus-match
const_fid
Same as plink –const-fid
control
Same as plink –control
counts
Same as plink –counts
covar
Same as plink –covar
covar_name
Same as plink –covar-name
covar_number
Same as plink –covar-number
cow
Same as plink –cow
d
Same as plink –d
data
Same as plink –data
debug
Same as plink –debug
decompress
Same as plink –decompress
dfam
Same as plink –dfam
distance
Same as plink –distance
distance_exp
Same as plink –distance-exp
distance_matrix
Same as plink –distance-matrix
dog
Same as plink –dog
dominant
Same as plink –dominant
dosage
Same as plink –dosage
double_id
Same as plink –double-id
dprime
Same as plink –dprime
dummy
Same as plink –dummy
dummy_coding
Same as plink –dummy-coding
each_versus_others
Same as plink –each-versus-others
each_vs_others
Same as plink –each-vs-others
epistasis
Same as plink –epistasis
epistasis_summary_merge
Same as plink –epistasis-summary-merge
exclude
Same as plink –exclude
exclude_before_extract
Same as plink –exclude-before-extract
exclude_snp
Same as plink –exclude-snp
exclude_snps
Same as plink –exclude-snps
extract
Same as plink –extract
fam
Same as plink –fam
family
Same as plink –family
fast_epistasis
Same as plink –fast-epistasis
fid
Same as plink –fid
file
Same as plink –file
fill_missing_a2
Same as plink –fill-missing-a2
filter
Same as plink –filter
filter_cases
Same as plink –filter-cases
filter_controls
Same as plink –filter-controls
filter_females
Same as plink –filter-females
filter_founders
Same as plink –filter-founders
filter_males
Same as plink –filter-males
filter_nonfounders
Same as plink –filter-nonfounders
fisher
Same as plink –fisher
flip
Same as plink –flip
flip_scan
Same as plink –flip-scan
flip_scan_threshold
Same as plink –flip-scan-threshold
flip_scan_verbose
Same as plink –flip-scan-verbose
flip_scan_window
Same as plink –flip-scan-window
flip_scan_window_kb
Same as plink –flip-scan-window-kb
flip_subset
Same as plink –flip-subset
freq
Same as plink –freq
freqx
Same as plink –freqx
from
Same as plink –from
from_bp
Same as plink –from-bp
from_kb
Same as plink –from-kb
from_mb
Same as plink –from-mb
frqx
Same as plink –frqx
fst
Same as plink –fst
gap
Same as plink –gap
gates
Same as plink –gates
gc
Same as plink –gc
gen
Same as plink –gen
gene
Same as plink –gene
gene_all
Same as plink –gene-all
gene_list
Same as plink –gene-list
gene_list_border
Same as plink –gene-list-border
gene_report
Same as plink –gene-report
gene_report_empty
Same as plink –gene-report-empty
gene_report_snp_field
Same as plink –gene-report-snp-field
gene_subset
Same as plink –gene-subset
genedrop
Same as plink –genedrop
genepi
Same as plink –genepi
geno
Same as plink –geno
genome
Same as plink –genome
genome_full
Same as plink –genome-full
genome_lists
Same as plink –genome-lists
genome_minimal
Same as plink –genome-minimal
genotypic
Same as plink –genotypic
gfile
Same as plink –gfile
gplink
Same as plink –gplink
grm
Same as plink –grm
grm_bin
Same as plink –grm-bin
grm_gz
Same as plink –grm-gz
group_avg
Same as plink –group-avg
groupdist
Same as plink –groupdist
gxe
Same as plink –gxe
hap...
Same as plink –hap...
hap
Same as plink –hap
hap_assoc
Same as plink –hap-assoc
hap_freq
Same as plink –hap-freq
hap_impute
Same as plink –hap-impute
hap_max_phase
Same as plink –hap-max-phase
hap_min_phase_prob
Same as plink –hap-min-phase-prob
hap_miss
Same as plink –hap-miss
hap_phase
Same as plink –hap-phase
hap_phase_wide
Same as plink –hap-phase-wide
hap_pp
Same as plink –hap-pp
hap_snps
Same as plink –hap-snps
hap_tdt
Same as plink –hap-tdt
hap_window
Same as plink –hap-window
hard_call_threshold
Same as plink –hard-call-threshold
hardy2
Same as plink –hardy2
hardy
Same as plink –hardy
help
Same as plink –help
het
Same as plink –het
hethom
Same as plink –hethom
hide_covar
Same as plink –hide-covar
homog
Same as plink –homog
homozyg
Same as plink –homozyg
homozyg_density
Same as plink –homozyg-density
homozyg_gap
Same as plink –homozyg-gap
homozyg_group
Same as plink –homozyg-group
homozyg_het
Same as plink –homozyg-het
homozyg_include_missing
Same as plink –homozyg-include-missing
homozyg_kb
Same as plink –homozyg-kb
homozyg_match
Same as plink –homozyg-match
homozyg_snp
Same as plink –homozyg-snp
homozyg_verbose
Same as plink –homozyg-verbose
homozyg_window_het
Same as plink –homozyg-window-het
homozyg_window_kb
Same as plink –homozyg-window-kb
homozyg_window_missing
Same as plink –homozyg-window-missing
homozyg_window_snp
Same as plink –homozyg-window-snp
homozyg_window_threshold
Same as plink –homozyg-window-threshold
horse
Same as plink –horse
hwe
Same as plink –hwe
hwe_all
Same as plink –hwe-all
ibc
Same as plink –ibc
ibm
Same as plink –ibm
ibs_matrix
Same as plink –ibs-matrix
ibs_test
Same as plink –ibs-test
id_delim
Same as plink –id-delim
id_dict
Same as plink –id-dict
id_match
Same as plink –id-match
iid
Same as plink –iid
impossible
Same as plink –impossible
impute_sex
Same as plink –impute-sex
ind_major
Same as plink –ind-major
indep
Same as plink –indep
indep_pairphase
Same as plink –indep-pairphase
indep_pairwise
Same as plink –indep-pairwise
independent_effect
Same as plink –independent-effect
indiv_sort
Same as plink –indiv-sort
inter_chr
Same as plink –inter-chr
interaction
Same as plink –interaction
je_cellmin
Same as plink –je-cellmin
keep
Same as plink –keep
keep_allele_order
Same as plink –keep-allele-order
keep_autoconv
Same as plink –keep-autoconv
keep_before_remove
Same as plink –keep-before-remove
keep_cluster_names
Same as plink –keep-cluster-names
keep_clusters
Same as plink –keep-clusters
keep_fam
Same as plink –keep-fam
lambda
Same as plink –lambda
lasso
Same as plink –lasso
lasso_select_covars
Same as plink –lasso-select-covars
ld
Same as plink –ld
ld_snp
Same as plink –ld-snp
ld_snp_list
Same as plink –ld-snp-list
ld_snps
Same as plink –ld-snps
ld_window
Same as plink –ld-window
ld_window_kb
Same as plink –ld-window-kb
ld_window_r2
Same as plink –ld-window-r2
ld_xchr
Same as plink –ld-xchr
lfile
Same as plink –lfile
liability
Same as plink –liability
linear
Same as plink –linear
list
Same as plink –list
list_23_indels
Same as plink –list-23-indels
list_all
Same as plink –list-all
logistic
Same as plink –logistic
lookup...
Same as plink –lookup...
lookup
Same as plink –lookup
lookup_gene
Same as plink –lookup-gene
lookup_list
Same as plink –lookup-list
loop_assoc
Same as plink –loop-assoc
maf
Same as plink –maf
maf_succ
Same as plink –maf-succ
make_bed
Same as plink –make-bed
make_founders
Same as plink –make-founders
make_grm
Same as plink –make-grm
make_grm_bin
Same as plink –make-grm-bin
make_grm_gz
Same as plink –make-grm-gz
make_just_bim
Same as plink –make-just-bim
make_just_fam
Same as plink –make-just-fam
make_perm_pheno
Same as plink –make-perm-pheno
make_pheno
Same as plink –make-pheno
make_rel
Same as plink –make-rel
make_set
Same as plink –make-set
make_set_border
Same as plink –make-set-border
make_set_collapse_group
Same as plink –make-set-collapse-group
make_set_complement_all
Same as plink –make-set-complement-all
make_set_complement_group
Same as plink –make-set-complement-group
map
Same as plink –map
mat
Same as plink –mat
match
Same as plink –match
match_type
Same as plink –match-type
matrix
Same as plink –matrix
max
Same as plink –max
max_maf
Same as plink –max-maf
mc
Same as plink –mc
mcc
Same as plink –mcc
mcovar
Same as plink –mcovar
mds_cluster
Same as plink –mds-cluster
mds_plot
Same as plink –mds-plot
me
Same as plink –me
me_exclude_one
Same as plink –me-exclude-one
memory
Same as plink –memory
mendel
Same as plink –mendel
mendel_duos
Same as plink –mendel-duos
mendel_multigen
Same as plink –mendel-multigen
merge
Same as plink –merge
merge_equal_pos
Same as plink –merge-equal-pos
merge_list
Same as plink –merge-list
merge_mode
Same as plink –merge-mode
merge_x
Same as plink –merge-x
meta_analysis
Same as plink –meta-analysis
meta_analysis_..._field
Same as plink –meta-analysis-...-field
mfilter
Same as plink –mfilter
mh
Same as plink –mh
mhf
Same as plink –mhf
min
Same as plink –min
mind
Same as plink –mind
mishap_window
Same as plink –mishap-window
missing
Same as plink –missing
missing_code
Same as plink –missing-code
missing_genotype
Same as plink –missing-genotype
missing_phenotype
Same as plink –missing-phenotype
missing_var_code
Same as plink –missing-var-code
mlma
Same as plink –mlma
mlma_loco
Same as plink –mlma-loco
mlma_no_adj_covar
Same as plink –mlma-no-adj-covar
model
Same as plink –model
model_dom
Same as plink –model-dom
model_gen
Same as plink –model-gen
model_rec
Same as plink –model-rec
model_trend
Same as plink –model-trend
mouse
Same as plink –mouse
mperm
Same as plink –mperm
mperm_save
Same as plink –mperm-save
mperm_save_all
Same as plink –mperm-save-all
mpheno
Same as plink –mpheno
must_have_sex
Same as plink –must-have-sex
mwithin
Same as plink –mwithin
neighbour
Same as plink –neighbour
no_fid
Same as plink –no-fid
no_parents
Same as plink –no-parents
no_pheno
Same as plink –no-pheno
no_sex
Same as plink –no-sex
no_snp
Same as plink –no-snp
no_x_sex
Same as plink –no-x-sex
nonfounders
Same as plink –nonfounders
nop
Same as plink –nop
not_chr
Same as plink –not-chr
nudge
Same as plink –nudge
null_group
Same as plink –null-group
null_snp
Same as plink –null-snp
oblig_cluster
Same as plink –oblig-cluster
oblig_clusters
Same as plink –oblig-clusters
oblig_missing
Same as plink –oblig-missing
out
Same as plink –out
output_chr
Same as plink –output-chr
output_missing_genotype
Same as plink –output-missing-genotype
output_missing_phenotype
Same as plink –output-missing-phenotype
oxford_pheno_name
Same as plink –oxford-pheno-name
parallel
Same as plink –parallel
parameters
Same as plink –parameters
parentdt1
Same as plink –parentdt1
parentdt2
Same as plink –parentdt2
pat
Same as plink –pat
pca
Same as plink –pca
pca_cluster_names
Same as plink –pca-cluster-names
pca_clusters
Same as plink –pca-clusters
ped
Same as plink –ped
pedigree
Same as plink –pedigree
perm
Same as plink –perm
perm_batch_size
Same as plink –perm-batch-size
perm_count
Same as plink –perm-count
pfilter
Same as plink –pfilter
pheno
Same as plink –pheno
pheno_merge
Same as plink –pheno-merge
pheno_name
Same as plink –pheno-name
pick1
Same as plink –pick1
plist
Same as plink –plist
poo
Same as plink –poo
pool_size
Same as plink –pool-size
ppc
Same as plink –ppc
ppc_gap
Same as plink –ppc-gap
proxy_...
Same as plink –proxy-...
proxy_assoc
Same as plink –proxy-assoc
proxy_b_kb
Same as plink –proxy-b-kb
proxy_b_maxsnp
Same as plink –proxy-b-maxsnp
proxy_b_r2
Same as plink –proxy-b-r2
proxy_b_threshold
Same as plink –proxy-b-threshold
proxy_b_window
Same as plink –proxy-b-window
proxy_dosage
Same as plink –proxy-dosage
proxy_drop
Same as plink –proxy-drop
proxy_flanking
Same as plink –proxy-flanking
proxy_geno
Same as plink –proxy-geno
proxy_genotypic_concordance
Same as plink –proxy-genotypic-concordance
proxy_glm
Same as plink –proxy-glm
proxy_impute
Same as plink –proxy-impute
proxy_impute_threshold
Same as plink –proxy-impute-threshold
proxy_kb
Same as plink –proxy-kb
proxy_list
Same as plink –proxy-list
proxy_maf
Same as plink –proxy-maf
proxy_maxsnp
Same as plink –proxy-maxsnp
proxy_mhf
Same as plink –proxy-mhf
proxy_r2
Same as plink –proxy-r2
proxy_r2_no_filter
Same as plink –proxy-r2-no-filter
proxy_replace
Same as plink –proxy-replace
proxy_show_proxies
Same as plink –proxy-show-proxies
proxy_sub_maxsnp
Same as plink –proxy-sub-maxsnp
proxy_sub_r2
Same as plink –proxy-sub-r2
proxy_tdt
Same as plink –proxy-tdt
proxy_verbose
Same as plink –proxy-verbose
proxy_window
Same as plink –proxy-window
prune
Same as plink –prune
q_score_file
Same as plink –q-score-file
q_score_range
Same as plink –q-score-range
qfam...
Same as plink –qfam...
qmatch
Same as plink –qmatch
qq_plot
Same as plink –qq-plot
qt
Same as plink –qt
qt_means
Same as plink –qt-means
qual_geno_...
Same as plink –qual-geno-...
qual_geno_max_threshold
Same as plink –qual-geno-max-threshold
qual_geno_scores
Same as plink –qual-geno-scores
qual_geno_threshold
Same as plink –qual-geno-threshold
qual_max_threshold
Same as plink –qual-max-threshold
qual_scores
Same as plink –qual-scores
qual_threshold
Same as plink –qual-threshold
r2
Same as plink –r2
r
Same as plink –r
range
Same as plink –range
rank
Same as plink –rank
read_dists
Same as plink –read-dists
read_freq
Same as plink –read-freq
read_genome
Same as plink –read-genome
read_genome_list
Same as plink –read-genome-list
read_genome_minimal
Same as plink –read-genome-minimal
recessive
Same as plink –recessive
recode12
Same as plink –recode12
recode
Same as plink –recode
recodeA
Same as plink –recodeA
recodeAD
Same as plink –recodeAD
recodeHV
Same as plink –recodeHV
recode_allele
Same as plink –recode-allele
recode_beagle
Same as plink –recode-beagle
recode_bimbam
Same as plink –recode-bimbam
recode_fastphase
Same as plink –recode-fastphase
recode_lgen
Same as plink –recode-lgen
recode_rlist
Same as plink –recode-rlist
recode_structure
Same as plink –recode-structure
recode_vcf
Same as plink –recode-vcf
recode_whap
Same as plink –recode-whap
reference
Same as plink –reference
reference_allele
Same as plink –reference-allele
regress_distance
Same as plink –regress-distance
regress_pcs
Same as plink –regress-pcs
regress_rel
Same as plink –regress-rel
rel_check
Same as plink –rel-check
rel_cutoff
Same as plink –rel-cutoff
remove
Same as plink –remove
remove_cluster_names
Same as plink –remove-cluster-names
remove_clusters
Same as plink –remove-clusters
remove_fam
Same as plink –remove-fam
rerun
Same as plink –rerun
rice
Same as plink –rice
sample
Same as plink –sample
score
Same as plink –score
score_no_mean_imputation
Same as plink –score-no-mean-imputation
script
Same as plink –script
seed
Same as plink –seed
set
Same as plink –set
set_by_all
Same as plink –set-by-all
set_collapse_all
Same as plink –set-collapse-all
set_hh_missing
Same as plink –set-hh-missing
set_max
Same as plink –set-max
set_me_missing
Same as plink –set-me-missing
set_missing_nonsnp_ids
Same as plink –set-missing-nonsnp-ids
set_missing_snp_ids
Same as plink –set-missing-snp-ids
set_missing_var_ids
Same as plink –set-missing-var-ids
set_names
Same as plink –set-names
set_p
Same as plink –set-p
set_r2
Same as plink –set-r2
set_r2_phase
Same as plink –set-r2-phase
set_table
Same as plink –set-table
set_test
Same as plink –set-test
sex
Same as plink –sex
sheep
Same as plink –sheep
show_tags
Same as plink –show-tags
silent
Same as plink –silent
simulate
Same as plink –simulate
simulate_haps
Same as plink –simulate-haps
simulate_label
Same as plink –simulate-label
simulate_missing
Same as plink –simulate-missing
simulate_n
Same as plink –simulate-n
simulate_ncases
Same as plink –simulate-ncases
simulate_ncontrols
Same as plink –simulate-ncontrols
simulate_prevalence
Same as plink –simulate-prevalence
simulate_qt
Same as plink –simulate-qt
simulate_tags
Same as plink –simulate-tags
snp
Same as plink –snp
snps
Same as plink –snps
snps_only
Same as plink –snps-only
specific_haplotype
Same as plink –specific-haplotype
split_x
Same as plink –split-x
standard_beta
Same as plink –standard-beta
subset
Same as plink –subset
swap_parents
Same as plink –swap-parents
swap_sibs
Same as plink –swap-sibs
swap_unrel
Same as plink –swap-unrel
tab
Same as plink –tab
tag_kb
Same as plink –tag-kb
tag_mode2
Same as plink –tag-mode2
tag_r2
Same as plink –tag-r2
tail_pheno
Same as plink –tail-pheno
tdt
Same as plink –tdt
test_all
Same as plink –test-all
test_mishap
Same as plink –test-mishap
test_missing
Same as plink –test-missing
test_snp
Same as plink –test-snp
tests
Same as plink –tests
tfam
Same as plink –tfam
tfile
Same as plink –tfile
thin
Same as plink –thin
thin_count
Same as plink –thin-count
threads
Same as plink –threads
to
Same as plink –to
to_bp
Same as plink –to-bp
to_kb
Same as plink –to-kb
to_mb
Same as plink –to-mb
tped
Same as plink –tped
transpose
Same as plink –transpose
trend
Same as plink –trend
tucc
Same as plink –tucc
twolocus
Same as plink –twolocus
unbounded
Same as plink –unbounded
unrelated_heritability
Same as plink –unrelated-heritability
update_alleles
Same as plink –update-alleles
update_chr
Same as plink –update-chr
update_cm
Same as plink –update-cm
update_ids
Same as plink –update-ids
update_map
Same as plink –update-map
update_name
Same as plink –update-name
update_parents
Same as plink –update-parents
update_sex
Same as plink –update-sex
vcf
Same as plink –vcf
vcf_filter
Same as plink –vcf-filter
vcf_half_call
Same as plink –vcf-half-call
vcf_idspace_to
Same as plink –vcf-idspace-to
vcf_min_qual
Same as plink –vcf-min-qual
vegas
Same as plink –vegas
version
Same as plink –version
vif
Same as plink –vif
whap
Same as plink –whap
window
Same as plink –window
with_freqs
Same as plink –with-freqs
with_phenotype
Same as plink –with-phenotype
with_reference
Same as plink –with-reference
within
Same as plink –within
write_cluster
Same as plink –write-cluster
write_covar
Same as plink –write-covar
write_dosage
Same as plink –write-dosage
write_set
Same as plink –write-set
write_set_r2
Same as plink –write-set-r2
write_snplist
Same as plink –write-snplist
xchr_model
Same as plink –xchr-model
zero_cluster
Same as plink –zero-cluster
zero_cms
Same as plink –zero-cms
one
Same as plink –1
twothreefile
Same as plink –23file
wait
Logical. If FALSE, the plink process will fork into the background.
stdout
Passed to system2, see its documentation.
stderr
Passed to system2, see its documentation.
plinkcollFileStems
A character vector of all bed file stems you want to pass to plink.
Details
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
kindlychung/CollapsABEL documentation built on May 20, 2019, 9:57 a.m.
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Description Usage Arguments Details
View source: R/getPlinkParam.R
Description
Get a list of parameters for passing to plinkr
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 | getPlinkParam(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)
|
Arguments
D |
Same as plink –D |
K |
Same as plink –K |
a1_allele |
Same as plink –a1-allele |
a2_allele |
Same as plink –a2-allele |
adjust |
Same as plink –adjust |
all |
Same as plink –all |
all_pheno |
Same as plink –all-pheno |
allele1234 |
Same as plink –allele1234 |
alleleACGT |
Same as plink –alleleACGT |
allele_count |
Same as plink –allele-count |
allow_extra_chr |
Same as plink –allow-extra-chr |
allow_no_sex |
Same as plink –allow-no-sex |
alt_group |
Same as plink –alt-group |
alt_snp |
Same as plink –alt-snp |
annotate |
Same as plink –annotate |
annotate_snp_field |
Same as plink –annotate-snp-field |
aperm |
Same as plink –aperm |
assoc |
Same as plink –assoc |
attrib |
Same as plink –attrib |
attrib_indiv |
Same as plink –attrib-indiv |
autosome |
Same as plink –autosome |
autosome_num |
Same as plink –autosome-num |
autosome_xy |
Same as plink –autosome-xy |
bcf |
Same as plink –bcf |
bd |
Same as plink –bd |
bed |
Same as plink –bed |
beta |
Same as plink –beta |
bfile |
Same as plink –bfile |
bgen |
Same as plink –bgen |
biallelic_only |
Same as plink –biallelic-only |
bim |
Same as plink –bim |
blocks |
Same as plink –blocks |
blocks_inform_frac |
Same as plink –blocks-inform-frac |
blocks_max_kb |
Same as plink –blocks-max-kb |
blocks_min_maf |
Same as plink –blocks-min-maf |
blocks_recomb_highci |
Same as plink –blocks-recomb-highci |
blocks_strong_highci |
Same as plink –blocks-strong-highci |
blocks_strong_lowci |
Same as plink –blocks-strong-lowci |
bmerge |
Same as plink –bmerge |
border |
Same as plink –border |
bp_space |
Same as plink –bp-space |
case_only |
Same as plink –case-only |
cc |
Same as plink –cc |
cell |
Same as plink –cell |
cfile |
Same as plink –cfile |
chap |
Same as plink –chap |
check_sex |
Same as plink –check-sex |
chr |
Same as plink –chr |
chr_set |
Same as plink –chr-set |
ci |
Same as plink –ci |
clump |
Same as plink –clump |
clump_allow_overlap |
Same as plink –clump-allow-overlap |
clump_annotate |
Same as plink –clump-annotate |
clump_best |
Same as plink –clump-best |
clump_field |
Same as plink –clump-field |
clump_index_first |
Same as plink –clump-index-first |
clump_kb |
Same as plink –clump-kb |
clump_p1 |
Same as plink –clump-p1 |
clump_p2 |
Same as plink –clump-p2 |
clump_r2 |
Same as plink –clump-r2 |
clump_range |
Same as plink –clump-range |
clump_range_border |
Same as plink –clump-range-border |
clump_replicate |
Same as plink –clump-replicate |
clump_snp_field |
Same as plink –clump-snp-field |
clump_verbose |
Same as plink –clump-verbose |
cluster |
Same as plink –cluster |
cluster_missing |
Same as plink –cluster-missing |
cm_map |
Same as plink –cm-map |
cnv_blue |
Same as plink –cnv-blue |
cnv_border |
Same as plink –cnv-border |
cnv_brown |
Same as plink –cnv-brown |
cnv_check_no_overlap |
Same as plink –cnv-check-no-overlap |
cnv_count |
Same as plink –cnv-count |
cnv_del |
Same as plink –cnv-del |
cnv_disrupt |
Same as plink –cnv-disrupt |
cnv_drop_no_segment |
Same as plink –cnv-drop-no-segment |
cnv_dup |
Same as plink –cnv-dup |
cnv_enrichment_test |
Same as plink –cnv-enrichment-test |
cnv_exclude |
Same as plink –cnv-exclude |
cnv_exclude_off_by_1 |
Same as plink –cnv-exclude-off-by-1 |
cnv_freq_excldue_above |
Same as plink –cnv-freq-excldue-above |
cnv_freq_excldue_below |
Same as plink –cnv-freq-excldue-below |
cnv_freq_excldue_exact |
Same as plink –cnv-freq-excldue-exact |
cnv_freq_exclude_above |
Same as plink –cnv-freq-exclude-above |
cnv_freq_exclude_below |
Same as plink –cnv-freq-exclude-below |
cnv_freq_exclude_exact |
Same as plink –cnv-freq-exclude-exact |
cnv_freq_incldue_exact |
Same as plink –cnv-freq-incldue-exact |
cnv_freq_include_exact |
Same as plink –cnv-freq-include-exact |
cnv_freq_method2 |
Same as plink –cnv-freq-method2 |
cnv_freq_overlap |
Same as plink –cnv-freq-overlap |
cnv_green |
Same as plink –cnv-green |
cnv_indiv_perm |
Same as plink –cnv-indiv-perm |
cnv_intersect |
Same as plink –cnv-intersect |
cnv_kb |
Same as plink –cnv-kb |
cnv_list |
Same as plink –cnv-list |
cnv_make_map |
Same as plink –cnv-make-map |
cnv_max_kb |
Same as plink –cnv-max-kb |
cnv_max_score |
Same as plink –cnv-max-score |
cnv_max_sites |
Same as plink –cnv-max-sites |
cnv_overlap |
Same as plink –cnv-overlap |
cnv_red |
Same as plink –cnv-red |
cnv_region_overlap |
Same as plink –cnv-region-overlap |
cnv_report_regions |
Same as plink –cnv-report-regions |
cnv_score |
Same as plink –cnv-score |
cnv_seglist |
Same as plink –cnv-seglist |
cnv_sites |
Same as plink –cnv-sites |
cnv_subset |
Same as plink –cnv-subset |
cnv_test |
Same as plink –cnv-test |
cnv_test_1sided |
Same as plink –cnv-test-1sided |
cnv_test_2sided |
Same as plink –cnv-test-2sided |
cnv_test_region |
Same as plink –cnv-test-region |
cnv_test_window |
Same as plink –cnv-test-window |
cnv_track |
Same as plink –cnv-track |
cnv_union_overlap |
Same as plink –cnv-union-overlap |
cnv_unique |
Same as plink –cnv-unique |
cnv_verbose_report_regions |
Same as plink –cnv-verbose-report-regions |
cnv_write |
Same as plink –cnv-write |
cnv_write_freq |
Same as plink –cnv-write-freq |
complement_sets |
Same as plink –complement-sets |
compound_genotypes |
Same as plink –compound-genotypes |
compress |
Same as plink –compress |
condition |
Same as plink –condition |
condition_list |
Same as plink –condition-list |
consensus_match |
Same as plink –consensus-match |
const_fid |
Same as plink –const-fid |
control |
Same as plink –control |
counts |
Same as plink –counts |
covar |
Same as plink –covar |
covar_name |
Same as plink –covar-name |
covar_number |
Same as plink –covar-number |
cow |
Same as plink –cow |
d |
Same as plink –d |
data |
Same as plink –data |
debug |
Same as plink –debug |
decompress |
Same as plink –decompress |
dfam |
Same as plink –dfam |
distance |
Same as plink –distance |
distance_exp |
Same as plink –distance-exp |
distance_matrix |
Same as plink –distance-matrix |
dog |
Same as plink –dog |
dominant |
Same as plink –dominant |
dosage |
Same as plink –dosage |
double_id |
Same as plink –double-id |
dprime |
Same as plink –dprime |
dummy |
Same as plink –dummy |
dummy_coding |
Same as plink –dummy-coding |
each_versus_others |
Same as plink –each-versus-others |
each_vs_others |
Same as plink –each-vs-others |
epistasis |
Same as plink –epistasis |
epistasis_summary_merge |
Same as plink –epistasis-summary-merge |
exclude |
Same as plink –exclude |
exclude_before_extract |
Same as plink –exclude-before-extract |
exclude_snp |
Same as plink –exclude-snp |
exclude_snps |
Same as plink –exclude-snps |
extract |
Same as plink –extract |
fam |
Same as plink –fam |
family |
Same as plink –family |
fast_epistasis |
Same as plink –fast-epistasis |
fid |
Same as plink –fid |
file |
Same as plink –file |
fill_missing_a2 |
Same as plink –fill-missing-a2 |
filter |
Same as plink –filter |
filter_cases |
Same as plink –filter-cases |
filter_controls |
Same as plink –filter-controls |
filter_females |
Same as plink –filter-females |
filter_founders |
Same as plink –filter-founders |
filter_males |
Same as plink –filter-males |
filter_nonfounders |
Same as plink –filter-nonfounders |
fisher |
Same as plink –fisher |
flip |
Same as plink –flip |
flip_scan |
Same as plink –flip-scan |
flip_scan_threshold |
Same as plink –flip-scan-threshold |
flip_scan_verbose |
Same as plink –flip-scan-verbose |
flip_scan_window |
Same as plink –flip-scan-window |
flip_scan_window_kb |
Same as plink –flip-scan-window-kb |
flip_subset |
Same as plink –flip-subset |
freq |
Same as plink –freq |
freqx |
Same as plink –freqx |
from |
Same as plink –from |
from_bp |
Same as plink –from-bp |
from_kb |
Same as plink –from-kb |
from_mb |
Same as plink –from-mb |
frqx |
Same as plink –frqx |
fst |
Same as plink –fst |
gap |
Same as plink –gap |
gates |
Same as plink –gates |
gc |
Same as plink –gc |
gen |
Same as plink –gen |
gene |
Same as plink –gene |
gene_all |
Same as plink –gene-all |
gene_list |
Same as plink –gene-list |
gene_list_border |
Same as plink –gene-list-border |
gene_report |
Same as plink –gene-report |
gene_report_empty |
Same as plink –gene-report-empty |
gene_report_snp_field |
Same as plink –gene-report-snp-field |
gene_subset |
Same as plink –gene-subset |
genedrop |
Same as plink –genedrop |
genepi |
Same as plink –genepi |
geno |
Same as plink –geno |
genome |
Same as plink –genome |
genome_full |
Same as plink –genome-full |
genome_lists |
Same as plink –genome-lists |
genome_minimal |
Same as plink –genome-minimal |
genotypic |
Same as plink –genotypic |
gfile |
Same as plink –gfile |
gplink |
Same as plink –gplink |
grm |
Same as plink –grm |
grm_bin |
Same as plink –grm-bin |
grm_gz |
Same as plink –grm-gz |
group_avg |
Same as plink –group-avg |
groupdist |
Same as plink –groupdist |
gxe |
Same as plink –gxe |
hap... |
Same as plink –hap... |
hap |
Same as plink –hap |
hap_assoc |
Same as plink –hap-assoc |
hap_freq |
Same as plink –hap-freq |
hap_impute |
Same as plink –hap-impute |
hap_max_phase |
Same as plink –hap-max-phase |
hap_min_phase_prob |
Same as plink –hap-min-phase-prob |
hap_miss |
Same as plink –hap-miss |
hap_phase |
Same as plink –hap-phase |
hap_phase_wide |
Same as plink –hap-phase-wide |
hap_pp |
Same as plink –hap-pp |
hap_snps |
Same as plink –hap-snps |
hap_tdt |
Same as plink –hap-tdt |
hap_window |
Same as plink –hap-window |
hard_call_threshold |
Same as plink –hard-call-threshold |
hardy2 |
Same as plink –hardy2 |
hardy |
Same as plink –hardy |
help |
Same as plink –help |
het |
Same as plink –het |
hethom |
Same as plink –hethom |
hide_covar |
Same as plink –hide-covar |
homog |
Same as plink –homog |
homozyg |
Same as plink –homozyg |
homozyg_density |
Same as plink –homozyg-density |
homozyg_gap |
Same as plink –homozyg-gap |
homozyg_group |
Same as plink –homozyg-group |
homozyg_het |
Same as plink –homozyg-het |
homozyg_include_missing |
Same as plink –homozyg-include-missing |
homozyg_kb |
Same as plink –homozyg-kb |
homozyg_match |
Same as plink –homozyg-match |
homozyg_snp |
Same as plink –homozyg-snp |
homozyg_verbose |
Same as plink –homozyg-verbose |
homozyg_window_het |
Same as plink –homozyg-window-het |
homozyg_window_kb |
Same as plink –homozyg-window-kb |
homozyg_window_missing |
Same as plink –homozyg-window-missing |
homozyg_window_snp |
Same as plink –homozyg-window-snp |
homozyg_window_threshold |
Same as plink –homozyg-window-threshold |
horse |
Same as plink –horse |
hwe |
Same as plink –hwe |
hwe_all |
Same as plink –hwe-all |
ibc |
Same as plink –ibc |
ibm |
Same as plink –ibm |
ibs_matrix |
Same as plink –ibs-matrix |
ibs_test |
Same as plink –ibs-test |
id_delim |
Same as plink –id-delim |
id_dict |
Same as plink –id-dict |
id_match |
Same as plink –id-match |
iid |
Same as plink –iid |
impossible |
Same as plink –impossible |
impute_sex |
Same as plink –impute-sex |
ind_major |
Same as plink –ind-major |
indep |
Same as plink –indep |
indep_pairphase |
Same as plink –indep-pairphase |
indep_pairwise |
Same as plink –indep-pairwise |
independent_effect |
Same as plink –independent-effect |
indiv_sort |
Same as plink –indiv-sort |
inter_chr |
Same as plink –inter-chr |
interaction |
Same as plink –interaction |
je_cellmin |
Same as plink –je-cellmin |
keep |
Same as plink –keep |
keep_allele_order |
Same as plink –keep-allele-order |
keep_autoconv |
Same as plink –keep-autoconv |
keep_before_remove |
Same as plink –keep-before-remove |
keep_cluster_names |
Same as plink –keep-cluster-names |
keep_clusters |
Same as plink –keep-clusters |
keep_fam |
Same as plink –keep-fam |
lambda |
Same as plink –lambda |
lasso |
Same as plink –lasso |
lasso_select_covars |
Same as plink –lasso-select-covars |
ld |
Same as plink –ld |
ld_snp |
Same as plink –ld-snp |
ld_snp_list |
Same as plink –ld-snp-list |
ld_snps |
Same as plink –ld-snps |
ld_window |
Same as plink –ld-window |
ld_window_kb |
Same as plink –ld-window-kb |
ld_window_r2 |
Same as plink –ld-window-r2 |
ld_xchr |
Same as plink –ld-xchr |
lfile |
Same as plink –lfile |
liability |
Same as plink –liability |
linear |
Same as plink –linear |
list |
Same as plink –list |
list_23_indels |
Same as plink –list-23-indels |
list_all |
Same as plink –list-all |
logistic |
Same as plink –logistic |
lookup... |
Same as plink –lookup... |
lookup |
Same as plink –lookup |
lookup_gene |
Same as plink –lookup-gene |
lookup_list |
Same as plink –lookup-list |
loop_assoc |
Same as plink –loop-assoc |
maf |
Same as plink –maf |
maf_succ |
Same as plink –maf-succ |
make_bed |
Same as plink –make-bed |
make_founders |
Same as plink –make-founders |
make_grm |
Same as plink –make-grm |
make_grm_bin |
Same as plink –make-grm-bin |
make_grm_gz |
Same as plink –make-grm-gz |
make_just_bim |
Same as plink –make-just-bim |
make_just_fam |
Same as plink –make-just-fam |
make_perm_pheno |
Same as plink –make-perm-pheno |
make_pheno |
Same as plink –make-pheno |
make_rel |
Same as plink –make-rel |
make_set |
Same as plink –make-set |
make_set_border |
Same as plink –make-set-border |
make_set_collapse_group |
Same as plink –make-set-collapse-group |
make_set_complement_all |
Same as plink –make-set-complement-all |
make_set_complement_group |
Same as plink –make-set-complement-group |
map |
Same as plink –map |
mat |
Same as plink –mat |
match |
Same as plink –match |
match_type |
Same as plink –match-type |
matrix |
Same as plink –matrix |
max |
Same as plink –max |
max_maf |
Same as plink –max-maf |
mc |
Same as plink –mc |
mcc |
Same as plink –mcc |
mcovar |
Same as plink –mcovar |
mds_cluster |
Same as plink –mds-cluster |
mds_plot |
Same as plink –mds-plot |
me |
Same as plink –me |
me_exclude_one |
Same as plink –me-exclude-one |
memory |
Same as plink –memory |
mendel |
Same as plink –mendel |
mendel_duos |
Same as plink –mendel-duos |
mendel_multigen |
Same as plink –mendel-multigen |
merge |
Same as plink –merge |
merge_equal_pos |
Same as plink –merge-equal-pos |
merge_list |
Same as plink –merge-list |
merge_mode |
Same as plink –merge-mode |
merge_x |
Same as plink –merge-x |
meta_analysis |
Same as plink –meta-analysis |
meta_analysis_..._field |
Same as plink –meta-analysis-...-field |
mfilter |
Same as plink –mfilter |
mh |
Same as plink –mh |
mhf |
Same as plink –mhf |
min |
Same as plink –min |
mind |
Same as plink –mind |
mishap_window |
Same as plink –mishap-window |
missing |
Same as plink –missing |
missing_code |
Same as plink –missing-code |
missing_genotype |
Same as plink –missing-genotype |
missing_phenotype |
Same as plink –missing-phenotype |
missing_var_code |
Same as plink –missing-var-code |
mlma |
Same as plink –mlma |
mlma_loco |
Same as plink –mlma-loco |
mlma_no_adj_covar |
Same as plink –mlma-no-adj-covar |
model |
Same as plink –model |
model_dom |
Same as plink –model-dom |
model_gen |
Same as plink –model-gen |
model_rec |
Same as plink –model-rec |
model_trend |
Same as plink –model-trend |
mouse |
Same as plink –mouse |
mperm |
Same as plink –mperm |
mperm_save |
Same as plink –mperm-save |
mperm_save_all |
Same as plink –mperm-save-all |
mpheno |
Same as plink –mpheno |
must_have_sex |
Same as plink –must-have-sex |
mwithin |
Same as plink –mwithin |
neighbour |
Same as plink –neighbour |
no_fid |
Same as plink –no-fid |
no_parents |
Same as plink –no-parents |
no_pheno |
Same as plink –no-pheno |
no_sex |
Same as plink –no-sex |
no_snp |
Same as plink –no-snp |
no_x_sex |
Same as plink –no-x-sex |
nonfounders |
Same as plink –nonfounders |
nop |
Same as plink –nop |
not_chr |
Same as plink –not-chr |
nudge |
Same as plink –nudge |
null_group |
Same as plink –null-group |
null_snp |
Same as plink –null-snp |
oblig_cluster |
Same as plink –oblig-cluster |
oblig_clusters |
Same as plink –oblig-clusters |
oblig_missing |
Same as plink –oblig-missing |
out |
Same as plink –out |
output_chr |
Same as plink –output-chr |
output_missing_genotype |
Same as plink –output-missing-genotype |
output_missing_phenotype |
Same as plink –output-missing-phenotype |
oxford_pheno_name |
Same as plink –oxford-pheno-name |
parallel |
Same as plink –parallel |
parameters |
Same as plink –parameters |
parentdt1 |
Same as plink –parentdt1 |
parentdt2 |
Same as plink –parentdt2 |
pat |
Same as plink –pat |
pca |
Same as plink –pca |
pca_cluster_names |
Same as plink –pca-cluster-names |
pca_clusters |
Same as plink –pca-clusters |
ped |
Same as plink –ped |
pedigree |
Same as plink –pedigree |
perm |
Same as plink –perm |
perm_batch_size |
Same as plink –perm-batch-size |
perm_count |
Same as plink –perm-count |
pfilter |
Same as plink –pfilter |
pheno |
Same as plink –pheno |
pheno_merge |
Same as plink –pheno-merge |
pheno_name |
Same as plink –pheno-name |
pick1 |
Same as plink –pick1 |
plist |
Same as plink –plist |
poo |
Same as plink –poo |
pool_size |
Same as plink –pool-size |
ppc |
Same as plink –ppc |
ppc_gap |
Same as plink –ppc-gap |
proxy_... |
Same as plink –proxy-... |
proxy_assoc |
Same as plink –proxy-assoc |
proxy_b_kb |
Same as plink –proxy-b-kb |
proxy_b_maxsnp |
Same as plink –proxy-b-maxsnp |
proxy_b_r2 |
Same as plink –proxy-b-r2 |
proxy_b_threshold |
Same as plink –proxy-b-threshold |
proxy_b_window |
Same as plink –proxy-b-window |
proxy_dosage |
Same as plink –proxy-dosage |
proxy_drop |
Same as plink –proxy-drop |
proxy_flanking |
Same as plink –proxy-flanking |
proxy_geno |
Same as plink –proxy-geno |
proxy_genotypic_concordance |
Same as plink –proxy-genotypic-concordance |
proxy_glm |
Same as plink –proxy-glm |
proxy_impute |
Same as plink –proxy-impute |
proxy_impute_threshold |
Same as plink –proxy-impute-threshold |
proxy_kb |
Same as plink –proxy-kb |
proxy_list |
Same as plink –proxy-list |
proxy_maf |
Same as plink –proxy-maf |
proxy_maxsnp |
Same as plink –proxy-maxsnp |
proxy_mhf |
Same as plink –proxy-mhf |
proxy_r2 |
Same as plink –proxy-r2 |
proxy_r2_no_filter |
Same as plink –proxy-r2-no-filter |
proxy_replace |
Same as plink –proxy-replace |
proxy_show_proxies |
Same as plink –proxy-show-proxies |
proxy_sub_maxsnp |
Same as plink –proxy-sub-maxsnp |
proxy_sub_r2 |
Same as plink –proxy-sub-r2 |
proxy_tdt |
Same as plink –proxy-tdt |
proxy_verbose |
Same as plink –proxy-verbose |
proxy_window |
Same as plink –proxy-window |
prune |
Same as plink –prune |
q_score_file |
Same as plink –q-score-file |
q_score_range |
Same as plink –q-score-range |
qfam... |
Same as plink –qfam... |
qmatch |
Same as plink –qmatch |
qq_plot |
Same as plink –qq-plot |
qt |
Same as plink –qt |
qt_means |
Same as plink –qt-means |
qual_geno_... |
Same as plink –qual-geno-... |
qual_geno_max_threshold |
Same as plink –qual-geno-max-threshold |
qual_geno_scores |
Same as plink –qual-geno-scores |
qual_geno_threshold |
Same as plink –qual-geno-threshold |
qual_max_threshold |
Same as plink –qual-max-threshold |
qual_scores |
Same as plink –qual-scores |
qual_threshold |
Same as plink –qual-threshold |
r2 |
Same as plink –r2 |
r |
Same as plink –r |
range |
Same as plink –range |
rank |
Same as plink –rank |
read_dists |
Same as plink –read-dists |
read_freq |
Same as plink –read-freq |
read_genome |
Same as plink –read-genome |
read_genome_list |
Same as plink –read-genome-list |
read_genome_minimal |
Same as plink –read-genome-minimal |
recessive |
Same as plink –recessive |
recode12 |
Same as plink –recode12 |
recode |
Same as plink –recode |
recodeA |
Same as plink –recodeA |
recodeAD |
Same as plink –recodeAD |
recodeHV |
Same as plink –recodeHV |
recode_allele |
Same as plink –recode-allele |
recode_beagle |
Same as plink –recode-beagle |
recode_bimbam |
Same as plink –recode-bimbam |
recode_fastphase |
Same as plink –recode-fastphase |
recode_lgen |
Same as plink –recode-lgen |
recode_rlist |
Same as plink –recode-rlist |
recode_structure |
Same as plink –recode-structure |
recode_vcf |
Same as plink –recode-vcf |
recode_whap |
Same as plink –recode-whap |
reference |
Same as plink –reference |
reference_allele |
Same as plink –reference-allele |
regress_distance |
Same as plink –regress-distance |
regress_pcs |
Same as plink –regress-pcs |
regress_rel |
Same as plink –regress-rel |
rel_check |
Same as plink –rel-check |
rel_cutoff |
Same as plink –rel-cutoff |
remove |
Same as plink –remove |
remove_cluster_names |
Same as plink –remove-cluster-names |
remove_clusters |
Same as plink –remove-clusters |
remove_fam |
Same as plink –remove-fam |
rerun |
Same as plink –rerun |
rice |
Same as plink –rice |
sample |
Same as plink –sample |
score |
Same as plink –score |
score_no_mean_imputation |
Same as plink –score-no-mean-imputation |
script |
Same as plink –script |
seed |
Same as plink –seed |
set |
Same as plink –set |
set_by_all |
Same as plink –set-by-all |
set_collapse_all |
Same as plink –set-collapse-all |
set_hh_missing |
Same as plink –set-hh-missing |
set_max |
Same as plink –set-max |
set_me_missing |
Same as plink –set-me-missing |
set_missing_nonsnp_ids |
Same as plink –set-missing-nonsnp-ids |
set_missing_snp_ids |
Same as plink –set-missing-snp-ids |
set_missing_var_ids |
Same as plink –set-missing-var-ids |
set_names |
Same as plink –set-names |
set_p |
Same as plink –set-p |
set_r2 |
Same as plink –set-r2 |
set_r2_phase |
Same as plink –set-r2-phase |
set_table |
Same as plink –set-table |
set_test |
Same as plink –set-test |
sex |
Same as plink –sex |
sheep |
Same as plink –sheep |
show_tags |
Same as plink –show-tags |
silent |
Same as plink –silent |
simulate |
Same as plink –simulate |
simulate_haps |
Same as plink –simulate-haps |
simulate_label |
Same as plink –simulate-label |
simulate_missing |
Same as plink –simulate-missing |
simulate_n |
Same as plink –simulate-n |
simulate_ncases |
Same as plink –simulate-ncases |
simulate_ncontrols |
Same as plink –simulate-ncontrols |
simulate_prevalence |
Same as plink –simulate-prevalence |
simulate_qt |
Same as plink –simulate-qt |
simulate_tags |
Same as plink –simulate-tags |
snp |
Same as plink –snp |
snps |
Same as plink –snps |
snps_only |
Same as plink –snps-only |
specific_haplotype |
Same as plink –specific-haplotype |
split_x |
Same as plink –split-x |
standard_beta |
Same as plink –standard-beta |
subset |
Same as plink –subset |
swap_parents |
Same as plink –swap-parents |
swap_sibs |
Same as plink –swap-sibs |
swap_unrel |
Same as plink –swap-unrel |
tab |
Same as plink –tab |
tag_kb |
Same as plink –tag-kb |
tag_mode2 |
Same as plink –tag-mode2 |
tag_r2 |
Same as plink –tag-r2 |
tail_pheno |
Same as plink –tail-pheno |
tdt |
Same as plink –tdt |
test_all |
Same as plink –test-all |
test_mishap |
Same as plink –test-mishap |
test_missing |
Same as plink –test-missing |
test_snp |
Same as plink –test-snp |
tests |
Same as plink –tests |
tfam |
Same as plink –tfam |
tfile |
Same as plink –tfile |
thin |
Same as plink –thin |
thin_count |
Same as plink –thin-count |
threads |
Same as plink –threads |
to |
Same as plink –to |
to_bp |
Same as plink –to-bp |
to_kb |
Same as plink –to-kb |
to_mb |
Same as plink –to-mb |
tped |
Same as plink –tped |
transpose |
Same as plink –transpose |
trend |
Same as plink –trend |
tucc |
Same as plink –tucc |
twolocus |
Same as plink –twolocus |
unbounded |
Same as plink –unbounded |
unrelated_heritability |
Same as plink –unrelated-heritability |
update_alleles |
Same as plink –update-alleles |
update_chr |
Same as plink –update-chr |
update_cm |
Same as plink –update-cm |
update_ids |
Same as plink –update-ids |
update_map |
Same as plink –update-map |
update_name |
Same as plink –update-name |
update_parents |
Same as plink –update-parents |
update_sex |
Same as plink –update-sex |
vcf |
Same as plink –vcf |
vcf_filter |
Same as plink –vcf-filter |
vcf_half_call |
Same as plink –vcf-half-call |
vcf_idspace_to |
Same as plink –vcf-idspace-to |
vcf_min_qual |
Same as plink –vcf-min-qual |
vegas |
Same as plink –vegas |
version |
Same as plink –version |
vif |
Same as plink –vif |
whap |
Same as plink –whap |
window |
Same as plink –window |
with_freqs |
Same as plink –with-freqs |
with_phenotype |
Same as plink –with-phenotype |
with_reference |
Same as plink –with-reference |
within |
Same as plink –within |
write_cluster |
Same as plink –write-cluster |
write_covar |
Same as plink –write-covar |
write_dosage |
Same as plink –write-dosage |
write_set |
Same as plink –write-set |
write_set_r2 |
Same as plink –write-set-r2 |
write_snplist |
Same as plink –write-snplist |
xchr_model |
Same as plink –xchr-model |
zero_cluster |
Same as plink –zero-cluster |
zero_cms |
Same as plink –zero-cms |
one |
Same as plink –1 |
twothreefile |
Same as plink –23file |
wait |
Logical. If FALSE, the plink process will fork into the background. |
stdout |
Passed to system2, see its documentation. |
stderr |
Passed to system2, see its documentation. |
plinkcollFileStems |
A character vector of all bed file stems you want to pass to plink. |
Details
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
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