Run plink --sexcheck to calculate the heterozygosity rate across X-chromosomal variants.
run_check_sex(indir, name, qcdir = indir, verbose = FALSE, path2plink = NULL, showPlinkOutput = TRUE)
indir | [character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files. |
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name | [character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam. |
qcdir | [character] /path/to/directory to save name.sexcheck as returned by plink --check-sex. User needs writing permission to qcdir. Per default qcdir=indir. |
verbose | [logical] If TRUE, progress info is printed to standard out. |
path2plink | [character] Absolute path to PLINK executable
(https://www.cog-genomics.org/plink/1.9/) i.e.
plink should be accesible as path2plink -h. The full name of the executable
should be specified: for windows OS, this means path/plink.exe, for unix
platforms this is path/plink. If not provided, assumed that PATH set-up works
and PLINK will be found by |
showPlinkOutput | [logical] If TRUE, plink log and error messages are printed to standard out. |
Both run_check_sex
and its evaluation
evaluate_check_sex
can simply be invoked by
check_sex
.
indir <- system.file("extdata", package="plinkQC") name <- 'data' qcdir <- tempdir() # the following code is not run on package build, as the path2plink on the # user system is not known.# NOT RUN { run <- run_check_sex(indir=indir, qcdir=qcdir, name=name) # }