overviewPerIndividualQC: Overview of per sample QC

In plinkQC: Genotype Quality Control with 'PLINK'

Overview of per sample QC

Description

overviewPerIndividualQC depicts results of perIndividualQC as intersection plots (via upset) and returns dataframes indicating which QC checks individuals failed or passed.

Usage

overviewPerIndividualQC(results_perIndividualQC, interactive = FALSE)

Arguments

results_perIndividualQC

[list] Output of perIndividualQC i.e. named [list] with i) sample_missingness containing a [vector] with sample IIDs failing the selected missingness threshold imissTh, ii) highIBD containing a [vector] with sample IIDs failing the selected relatedness threshold highIBDTh, iii) outlying_heterozygosity containing a [vector] with sample IIDs failing selected the heterozygosity threshold hetTh, iv) mismatched_sex containing a [vector] with the sample IIDs failing the sexcheck based on SNPSEX and selected femaleTh/maleTh, and v) p_sampleQC, a ggplot2-object 'containing' a sub-paneled plot with the QC-plots of check_sex, check_het_and_miss, and check_relatedness.

interactive

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_overview) via ggplot2::ggsave(p=p_overview, other_arguments) or pdf(outfile) print(p_overview) dev.off().

Value

Named [list] with i) nr_fail_samples: total number of samples [integer] failing perIndividualQC, ii) fail_QC containing a [data.frame] with samples that failed QC steps (excluding ancestry) with IID, FID, all QC steps applied by perIndividualQC (max=4), with entries=0 if passing the QC and entries=1 if failing that particular QC and iii) fail_QC_and_ancestry_exclusion containing a [data.frame] with samples that are excluded for ancestry and QC checks with IID, FID, QC_fail and Ancestry_exclusion, with entries=0 if passing and entries=1 if failing that check, iii) p_overview, a ggplot2-object 'containing' a sub-paneled plot with the QC-plots.

Examples

indir <- system.file("extdata", package="plinkQC")
qcdir <- tempdir()
name <- "data"
## Not run: 
fail_individuals <- perIndividualQC(qcdir=qcdir, indir=indir, name=name,
refSamplesFile=paste(qcdir, "/HapMap_ID2Pop.txt",sep=""),
refColorsFile=paste(qcdir, "/HapMap_PopColors.txt", sep=""),
prefixMergedDataset="data.HapMapIII", interactive=FALSE, verbose=FALSE,
do.run_check_het_and_miss=FALSE, do.run_check_relatedness=FALSE,
do.run_check_sex=FALSE)

overview <- overviewPerIndividualQC(fail_individuals)

## End(Not run)

plinkQC documentation built on Nov. 26, 2025, 1:07 a.m.