overviewPerMarkerQC depicts results of
an intersection plot (via
upset) and returns a
dataframe indicating which QC checks were failed or passed.
[list] Output of
[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().
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.
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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) ## End(Not run)
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