plinkr: A wrapper for plink

Description Usage Arguments

View source: R/0_plinkr.R

Description

A wrapper for plink

Usage

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plinkr(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,
  stdout = collenv$.plink_stdout, stderr = collenv$.plink_stderr,
  wait = TRUE)

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

stdout

Passed to system2, see its documentation.

stderr

Passed to system2, see its documentation.

wait

Logical. If FALSE, the plink process will fork into the background.


CollapsABEL documentation built on May 29, 2017, 9:43 a.m.