A utility script to recalculate the the frequency of the homozygous reference SNP by locus after some populations have been deleted
The locus metadata supplied by DArT has FreqHomRef included, but the frequency of the homozygous reference will change when some individuals are removed from the dataset. This script recalculates the FreqHomRef and places these recalculated values in the appropriate place in the genlight object. Note that the frequency of the homozygote reference SNPS is calculated from the individuals that could be scored.
utils.recalc.freqhomref(x, verbose = NULL)
x |
– name of the genlight object containing the SNP data [required] |
verbose |
– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2] |
The modified genlight object
Arthur Georges (Post to https://groups.google.com/d/forum/dartr)
utils.recalc.metrics for recalculating all metrics, utils.recalc.callrate for recalculating CallRate,
utils.recalc.avgpic for recalculating AvgPIC, utils.recalc.freqhomsnp for recalculating frequency of homozygous alternate,
utils.recalc.freqhet for recalculating frequency of heterozygotes, gl.recalc.maf for recalculating minor allele frequency,
gl.recalc.rdepth for recalculating average read depth
#result <- utils.recalc.freqhomref(testset.gl)
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