A utility script to recalculate the the minor allele frequency by locus, typically after some populations have been deleted
The locus metadata supplied by DArT does not have MAF included, so it is calculated and added to the locus.metadata by this script. The minimum allele frequency will change when some individuals are removed from the dataset. This script recalculates the MAF and places these recalculated values in the appropriate place in the genlight object.
utils.recalc.maf(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 dataset
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.avgpic for recalculating AvgPIC,
gl.recalc.rdepth for recalculating average read depth
#f <- dartR::utils.recalc.maf(testset.gl)
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