R/plinkcollr.R
In kindlychung/CollapsABEL: An R package for quantitative CDH analysis
Defines functions
plinkcollr
Documented in
plinkcollr
#' Apply plinkr to multiple files
#'
#' All the parameters of this function is documented in \code{\link{getPlinkParam}}.
#'
#' @import stringr
#' @export
#' @seealso \code{\link{getPlinkParam}} \code{\link{plinkr}}
#'
plinkcollr = function(
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=""
) {
paramList = mget(names(formals()),sys.frame(sys.nframe()))
# Should I wait for the process to finish?
wait = paramList$wait
paramList$wait = NULL
# stdout and stderr settings, default is to the R console
stdout = paramList$stdout
paramList$stdout = NULL
stderr = paramList$stderr
paramList$stderr = NULL
# get list of collapsed bed files
plinkcollFileStems = paramList$plinkcollFileStems
if(is.null(plinkcollFileStems)) stop("You must give a vector of bed files to apply plink upon")
# debugps("Recieved bed files:")
# debugpo(plinkcollFileStems)
if(grepl("bed$", plinkcollFileStems[1], perl=TRUE)) {
plinkcollFileStems = getstem(plinkcollFileStems)
# debugps('Removing .bed extension...')
# debugpo(plinkcollFileStems)
}
paramList$plinkcollFileStems = NULL
paramVector = unlist(paramList)
paramVector = paramVector[!is.null(paramVector)]
paramVector = str_trim(paramVector)
paramName = names(paramVector)
names(paramVector) = NULL
paramName = gsub("_", "-", paramName)
paramName = paste("--", paramName, sep="")
if("--one" %in% paramName) {
idx = which(paramName == "--one")
paramName[idx] = "--1"
}
if("--twothreefile" %in% paramName) {
idx = which(paramName == "--twothreefile")
paramName[idx] = "--23file"
}
nParam = length(paramName)
idxOdd = seq(1, nParam * 2, 2)
idxEven = seq(2, nParam * 2, 2)
paramNameThenValue = character(nParam * 2)
paramNameThenValue[idxOdd] = paramName
paramNameThenValue[idxEven] = paramVector
# debugps("Recieved parameters: ")
# debugpo(paramNameThenValue)
if("--out" %in% paramNameThenValue) stop("The 'out' option shouldn't be in thre batch mode")
if("--bfile" %in% paramNameThenValue) stop("The 'bfile' option shouldn't be in there batch mode")
nfiles = length(plinkcollFileStems)
nscanned = 0
for(bedFile in plinkcollFileStems) {
message(sprintf("Running plink on %s...", bedFile))
localParam = paramNameThenValue
localParam = c("--bfile", bedFile, "--out", bedFile, localParam)
ret = system2("plink", localParam, wait=wait, stdout=NULL, stderr=NULL)
# if(dbgtrigger()) cat("Return value from PLINK: ", ret, "\n")
if(ret != 0) stop("PLINK failed.")
nscanned = nscanned + 1
message(sprintf("Removing %s...", bedFile))
file.remove(sprintf("%s.bed", bedFile))
}
cat("\n")
}
kindlychung/CollapsABEL documentation built on May 20, 2019, 9:57 a.m.
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Defines functions plinkcollr
Documented in plinkcollr
#' Apply plinkr to multiple files
#'
#' All the parameters of this function is documented in \code{\link{getPlinkParam}}.
#'
#' @import stringr
#' @export
#' @seealso \code{\link{getPlinkParam}} \code{\link{plinkr}}
#'
plinkcollr = function(
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=""
) {
paramList = mget(names(formals()),sys.frame(sys.nframe()))
# Should I wait for the process to finish?
wait = paramList$wait
paramList$wait = NULL
# stdout and stderr settings, default is to the R console
stdout = paramList$stdout
paramList$stdout = NULL
stderr = paramList$stderr
paramList$stderr = NULL
# get list of collapsed bed files
plinkcollFileStems = paramList$plinkcollFileStems
if(is.null(plinkcollFileStems)) stop("You must give a vector of bed files to apply plink upon")
# debugps("Recieved bed files:")
# debugpo(plinkcollFileStems)
if(grepl("bed$", plinkcollFileStems[1], perl=TRUE)) {
plinkcollFileStems = getstem(plinkcollFileStems)
# debugps('Removing .bed extension...')
# debugpo(plinkcollFileStems)
}
paramList$plinkcollFileStems = NULL
paramVector = unlist(paramList)
paramVector = paramVector[!is.null(paramVector)]
paramVector = str_trim(paramVector)
paramName = names(paramVector)
names(paramVector) = NULL
paramName = gsub("_", "-", paramName)
paramName = paste("--", paramName, sep="")
if("--one" %in% paramName) {
idx = which(paramName == "--one")
paramName[idx] = "--1"
}
if("--twothreefile" %in% paramName) {
idx = which(paramName == "--twothreefile")
paramName[idx] = "--23file"
}
nParam = length(paramName)
idxOdd = seq(1, nParam * 2, 2)
idxEven = seq(2, nParam * 2, 2)
paramNameThenValue = character(nParam * 2)
paramNameThenValue[idxOdd] = paramName
paramNameThenValue[idxEven] = paramVector
# debugps("Recieved parameters: ")
# debugpo(paramNameThenValue)
if("--out" %in% paramNameThenValue) stop("The 'out' option shouldn't be in thre batch mode")
if("--bfile" %in% paramNameThenValue) stop("The 'bfile' option shouldn't be in there batch mode")
nfiles = length(plinkcollFileStems)
nscanned = 0
for(bedFile in plinkcollFileStems) {
message(sprintf("Running plink on %s...", bedFile))
localParam = paramNameThenValue
localParam = c("--bfile", bedFile, "--out", bedFile, localParam)
ret = system2("plink", localParam, wait=wait, stdout=NULL, stderr=NULL)
# if(dbgtrigger()) cat("Return value from PLINK: ", ret, "\n")
if(ret != 0) stop("PLINK failed.")
nscanned = nscanned + 1
message(sprintf("Removing %s...", bedFile))
file.remove(sprintf("%s.bed", bedFile))
}
cat("\n")
}
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