Run plink --missing to calculate missing genotype rates per individual.
run_check_missingness(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. |
---|---|
name | [character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam. |
qcdir | [character] /path/to/directory to save name.imiss as returned by plink --missing. 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. |
All, run_check_heterozygosity
,
run_check_missingness
and their evaluation by
evaluate_check_het_and_miss
can simply be invoked by
check_het_and_miss
.
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_missingnessness(indir=indir, qcdir=qcdir, name=name) # }