A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some populations have been deleted.
The locus metadata supplied by DArT has OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC included, but the allelec composition will change when some individuals are removed from the dataset and so the initial statistics will no longer apply. This script recalculates these statistics and places the recalculated values in the appropriate place in the genlight object.
utils.recalc.avgpic(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] |
If the locus metadata OneRatioRef|Snp, PICRef|Snp and/or AvgPIC do not exist, the script creates and populates them.
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.freqhomref for recalculating frequency of homozygous reference, 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
#out <- utils.recalc.avgpic(testset.gl)
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