From 64b539087fce3c0bab65648bb081f3d0b10cdbdb Mon Sep 17 00:00:00 2001 From: HannahVMeyer Date: Fri, 5 Feb 2021 14:32:18 -0500 Subject: [PATCH 1/2] extract_markers instead of keep, stick with plink names --- R/individualQC.R | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/R/individualQC.R b/R/individualQC.R index 69281d2..1c338b3 100755 --- a/R/individualQC.R +++ b/R/individualQC.R @@ -171,7 +171,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -226,7 +226,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) run_het <- run_check_heterozygosity(qcdir=qcdir, indir=indir, @@ -235,7 +235,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -290,7 +290,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -320,7 +320,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -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, + extract_markers=NULL, extract_markers=NULL, showPlinkOutput=TRUE) { if (run.check_sex) { @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) } @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) return(fail) @@ -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, + extract_markers=NULL, extract_markers=NULL, path2plink=NULL, showPlinkOutput=TRUE) { if (run.check_het_and_miss) { @@ -784,7 +784,7 @@ 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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) run_miss <- run_check_missingness(indir=indir, qcdir=qcdir, name=name, @@ -792,7 +792,7 @@ 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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) } @@ -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, + extract_markers=NULL, extract_markers=NULL, showPlinkOutput=TRUE) { if (run.check_relatedness) { @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) } @@ -1038,7 +1038,7 @@ check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset, highlight_legend = FALSE, keep_individuals=NULL, remove_individuals=NULL, - keep_markers=NULL, + extract_markers=NULL, extract_markers=NULL, path2plink=NULL, showPlinkOutput=TRUE) { if (run.check_ancestry) { @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) } From df6d050297cc0ce93b90ba8cdaa8fa53f40630b4 Mon Sep 17 00:00:00 2001 From: HannahVMeyer Date: Fri, 5 Feb 2021 14:32:18 -0500 Subject: [PATCH 2/2] extract_markers instead of keep, stick with plink names (#33) --- R/individualQC.R | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/R/individualQC.R b/R/individualQC.R index 69281d2..1c338b3 100755 --- a/R/individualQC.R +++ b/R/individualQC.R @@ -171,7 +171,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -226,7 +226,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) run_het <- run_check_heterozygosity(qcdir=qcdir, indir=indir, @@ -235,7 +235,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -290,7 +290,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -320,7 +320,7 @@ perIndividualQC <- function(indir, name, qcdir=indir, showPlinkOutput=showPlinkOutput, keep_individuals=keep_individuals, remove_individuals=remove_individuals, - keep_markers=keep_markers, + extract_markers=extract_markers, extract_markers=extract_markers, verbose=verbose) } @@ -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, + extract_markers=NULL, extract_markers=NULL, showPlinkOutput=TRUE) { if (run.check_sex) { @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) } @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) return(fail) @@ -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, + extract_markers=NULL, extract_markers=NULL, path2plink=NULL, showPlinkOutput=TRUE) { if (run.check_het_and_miss) { @@ -784,7 +784,7 @@ 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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) run_miss <- run_check_missingness(indir=indir, qcdir=qcdir, name=name, @@ -792,7 +792,7 @@ 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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) } @@ -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, + extract_markers=NULL, extract_markers=NULL, showPlinkOutput=TRUE) { if (run.check_relatedness) { @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) } @@ -1038,7 +1038,7 @@ check_ancestry <- function(indir, name, qcdir=indir, prefixMergedDataset, highlight_legend = FALSE, keep_individuals=NULL, remove_individuals=NULL, - keep_markers=NULL, + extract_markers=NULL, extract_markers=NULL, path2plink=NULL, showPlinkOutput=TRUE) { if (run.check_ancestry) { @@ -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, + extract_markers=extract_markers, extract_markers=extract_markers, showPlinkOutput=showPlinkOutput) }