plinkQC (version 0.2.2)

overviewPerMarkerQC: Overview of per marker QC

Description

overviewPerMarkerQC depicts results of perMarkerQC as an intersection plot (via upset) and returns a dataframe indicating which QC checks were failed or passed.

Usage

overviewPerMarkerQC(results_perMarkerQC, interactive = FALSE)

Arguments

results_perMarkerQC

[list] Output of perIndividualQC i.e. named [list] with i) fail_list, a named [list] with 1. SNP_missingness, containing SNP IDs failing the missingness threshold lmissTh, 2. hwe, containing SNP IDs failing the HWE exact test threshold hweTh and 3. maf, containing SNPs failing the MAF threshold mafTh/MAC threshold macTh and ii) p_markerQC, a ggplot2-object 'containing' a sub-paneled plot with the QC-plots of check_snp_missingness, check_hwe and check_maf

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_markers: total number of markers [integer] failing perMarkerQC, ii) fail_QC containing a [data.frame] with markers that failed QC steps: marker rsIDs in rows, columns are all QC steps applied by perMarkerQC (max=3), with entries=0 if passing the QC and entries=1 if failing that particular QC.

Examples

# NOT RUN {
indir <- system.file("extdata", package="plinkQC")
qcdir <- tempdir()
name <- "data"
path2plink <- '/path/to/plink'
# the following code is not run on package build, as the path2plink on the
# user system is not known.
# All quality control checks
# }
# NOT RUN {
fail_markers <- perMarkerQC(qcdir=qcdir, indir=indir, name=name,
interactive=FALSE, verbose=TRUE, path2plink=path2plink)
overview <- overviewPerMarkerQC(fail_markers)
# }