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Fixed naming
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HannahVMeyer authored and HannahVMeyer committed Feb 5, 2021
1 parent 1f76b4f commit 81b7576
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions R/individualQC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,7 @@ perIndividualQC <- function(indir, name, qcdir=indir,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
verbose=verbose)
}
Expand Down Expand Up @@ -226,7 +226,7 @@ perIndividualQC <- function(indir, name, qcdir=indir,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
verbose=verbose)
run_het <- run_check_heterozygosity(qcdir=qcdir, indir=indir,
Expand All @@ -235,7 +235,7 @@ perIndividualQC <- function(indir, name, qcdir=indir,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
verbose=verbose)
}
Expand Down Expand Up @@ -290,7 +290,7 @@ perIndividualQC <- function(indir, name, qcdir=indir,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
verbose=verbose)
}
Expand Down Expand Up @@ -320,7 +320,7 @@ perIndividualQC <- function(indir, name, qcdir=indir,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
verbose=verbose)
}
Expand Down Expand Up @@ -637,7 +637,7 @@ check_sex <- function(indir, name, qcdir=indir, maleTh=0.8, femaleTh=0.2,
path2plink=NULL,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
exclude_markers=NULL,
extract_markers=NULL,
showPlinkOutput=TRUE) {
if (run.check_sex) {
Expand All @@ -646,7 +646,7 @@ check_sex <- function(indir, name, qcdir=indir, maleTh=0.8, femaleTh=0.2,
path2plink=path2plink,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
Expand All @@ -668,7 +668,7 @@ check_sex <- function(indir, name, qcdir=indir, maleTh=0.8, femaleTh=0.2,
highlight_legend = highlight_legend,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
return(fail)
Expand Down Expand Up @@ -775,7 +775,7 @@ check_het_and_miss <- function(indir, name, qcdir=indir, imissTh=0.03, hetTh=3,
interactive=FALSE, verbose=FALSE,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
exclude_markers=NULL,
extract_markers=NULL,
path2plink=NULL, showPlinkOutput=TRUE) {
if (run.check_het_and_miss) {
Expand All @@ -784,15 +784,15 @@ check_het_and_miss <- function(indir, name, qcdir=indir, imissTh=0.03, hetTh=3,
path2plink=path2plink,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
run_miss <- run_check_missingness(indir=indir, qcdir=qcdir, name=name,
verbose=verbose,
path2plink=path2plink,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
Expand Down Expand Up @@ -899,7 +899,7 @@ check_relatedness <- function(indir, name, qcdir=indir, highIBDTh=0.1875,
mafThRelatedness=0.1, path2plink=NULL,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
exclude_markers=NULL,
extract_markers=NULL,
showPlinkOutput=TRUE) {
if (run.check_relatedness) {
Expand All @@ -910,7 +910,7 @@ check_relatedness <- function(indir, name, qcdir=indir, highIBDTh=0.1875,
highIBDTh=highIBDTh,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
Expand Down Expand Up @@ -1038,7 +1038,7 @@ check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset,
highlight_legend = FALSE,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
exclude_markers=NULL,
extract_markers=NULL,
path2plink=NULL, showPlinkOutput=TRUE) {
if (run.check_ancestry) {
Expand All @@ -1048,7 +1048,7 @@ check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset,
path2plink=path2plink,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
exclude_markers=exclude_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
Expand Down

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