overviewPerMarkerQC {plinkQC} | R Documentation |
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 |
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
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)