Usage
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
a1_allele
Same as plink --a1-allele
a2_allele
Same as plink --a2-allele
adjust
Same as plink --adjust
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
bfile
Same as plink --bfile
biallelic_only
Same as plink --biallelic-only
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
cfile
Same as plink --cfile
check_sex
Same as plink --check-sex
chr_set
Same as plink --chr-set
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
debug
Same as plink --debug
decompress
Same as plink --decompress
distance
Same as plink --distance
distance_exp
Same as plink --distance-exp
distance_matrix
Same as plink --distance-matrix
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
family
Same as plink --family
fast_epistasis
Same as plink --fast-epistasis
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_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
freqx
Same as plink --freqx
from_bp
Same as plink --from-bp
from_kb
Same as plink --from-kb
from_mb
Same as plink --from-mb
gates
Same as plink --gates
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
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_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
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
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_all
Same as plink --hwe-all
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
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_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_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_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_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
match
Same as plink --match
match_type
Same as plink --match-type
matrix
Same as plink --matrix
max_maf
Same as plink --max-maf
mcovar
Same as plink --mcovar
mds_cluster
Same as plink --mds-cluster
mds_plot
Same as plink --mds-plot
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
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_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
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
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
pca_cluster_names
Same as plink --pca-cluster-names
pca_clusters
Same as plink --pca-clusters
pedigree
Same as plink --pedigree
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
pool_size
Same as plink --pool-size
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_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
range
Same as plink --range
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
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
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
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
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
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
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
tfile
Same as plink --tfile
thin_count
Same as plink --thin-count
threads
Same as plink --threads
to_bp
Same as plink --to-bp
to_kb
Same as plink --to-kb
to_mb
Same as plink --to-mb
transpose
Same as plink --transpose
trend
Same as plink --trend
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_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
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
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.