A wrapper for plink. All the parameters of this function is documented in getPlinkParam
.
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 | 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 = "", stderr = "", wait = TRUE)
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