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Added options for keep/remove individuals, extract/exclude markers in…
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… individual qc functions; all tests passing, not implemented to actually filter yet (#33).
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@HannahVMeyer
HannahVMeyer committed Feb 5, 2021
1 parent 416f9fe commit 1f76b4f
Showing 1 changed file with 62 additions and 1 deletion.
63 changes: 62 additions & 1 deletion R/individualQC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -169,6 +169,10 @@ perIndividualQC <- function(indir, name, qcdir=indir,
run <- run_check_sex(indir=indir, qcdir=qcdir, name=name,
path2plink=path2plink,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
verbose=verbose)
}
if (do.evaluate_check_sex) {
Expand Down Expand Up @@ -220,11 +224,19 @@ perIndividualQC <- function(indir, name, qcdir=indir,
name=name,
path2plink=path2plink,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
verbose=verbose)
run_het <- run_check_heterozygosity(qcdir=qcdir, indir=indir,
name=name,
path2plink=path2plink,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
verbose=verbose)
}
if (do.evaluate_check_het_and_miss) {
Expand Down Expand Up @@ -276,6 +288,10 @@ perIndividualQC <- function(indir, name, qcdir=indir,
mafThRelatedness=mafThRelatedness,
genomebuild=genomebuild,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
verbose=verbose)
}
if (do.evaluate_check_relatedness) {
Expand All @@ -302,6 +318,10 @@ perIndividualQC <- function(indir, name, qcdir=indir,
prefixMergedDataset=prefixMergedDataset,
path2plink=path2plink,
showPlinkOutput=showPlinkOutput,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
verbose=verbose)
}
if (do.evaluate_check_ancestry) {
Expand Down Expand Up @@ -614,11 +634,20 @@ check_sex <- function(indir, name, qcdir=indir, maleTh=0.8, femaleTh=0.2,
highlight_color = "#c51b8a",
highlight_shape = 17,
highlight_legend = FALSE,
path2plink=NULL, showPlinkOutput=TRUE) {
path2plink=NULL,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
extract_markers=NULL,
showPlinkOutput=TRUE) {
if (run.check_sex) {
run_sex <- run_check_sex(indir=indir, qcdir=qcdir, name=name,
verbose=verbose,
path2plink=path2plink,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
fail <- evaluate_check_sex(qcdir=qcdir, name=name, externalSex=externalSex,
Expand All @@ -637,6 +666,10 @@ check_sex <- function(indir, name, qcdir=indir, maleTh=0.8, femaleTh=0.2,
highlight_color = highlight_color,
highlight_shape = highlight_shape,
highlight_legend = highlight_legend,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
return(fail)
}
Expand Down Expand Up @@ -740,15 +773,27 @@ check_het_and_miss <- function(indir, name, qcdir=indir, imissTh=0.03, hetTh=3,
highlight_shape = 17,
highlight_legend = FALSE,
interactive=FALSE, verbose=FALSE,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
extract_markers=NULL,
path2plink=NULL, showPlinkOutput=TRUE) {
if (run.check_het_and_miss) {
run_het <- run_check_heterozygosity(indir=indir,qcdir=qcdir, name=name,
verbose=verbose,
path2plink=path2plink,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_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,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
fail <- evaluate_check_het_and_miss(qcdir=qcdir, name=name, hetTh=hetTh,
Expand Down Expand Up @@ -852,13 +897,21 @@ check_relatedness <- function(indir, name, qcdir=indir, highIBDTh=0.1875,
run.check_relatedness=TRUE,
interactive=FALSE, verbose=FALSE,
mafThRelatedness=0.1, path2plink=NULL,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
extract_markers=NULL,
showPlinkOutput=TRUE) {
if (run.check_relatedness) {
run <- run_check_relatedness(indir=indir, qcdir=qcdir, name=name,
verbose=verbose,
mafThRelatedness=mafThRelatedness,
path2plink=path2plink,
highIBDTh=highIBDTh,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
fail <- evaluate_check_relatedness(qcdir=qcdir, name=name,
Expand Down Expand Up @@ -983,12 +1036,20 @@ check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset,
highlight_color = "#c51b8a",
highlight_shape = 17,
highlight_legend = FALSE,
keep_individuals=NULL,
remove_individuals=NULL,
keep_markers=NULL,
extract_markers=NULL,
path2plink=NULL, showPlinkOutput=TRUE) {
if (run.check_ancestry) {
run <- run_check_ancestry(indir=indir, qcdir=qcdir,
prefixMergedDataset=prefixMergedDataset,
verbose=verbose,
path2plink=path2plink,
keep_individuals=keep_individuals,
remove_individuals=remove_individuals,
keep_markers=keep_markers,
extract_markers=extract_markers,
showPlinkOutput=showPlinkOutput)
}
fail <- evaluate_check_ancestry(qcdir=qcdir, indir=indir, name=name,
Expand Down

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