plinkcollr: Apply plinkr to multiple files
In kindlychung/CollapsABEL: An R package for quantitative CDH analysis

All the parameters of this function is documented in getPlinkParam.

plinkcollr(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,
  plinkcollFileStems = NULL, wait = TRUE, stdout = "", stderr = "")