A utility script to recalculate the callrate by locus after some populations have been deleted
SNP datasets generated by DArT have missing values primarily arising from failure to call a SNP because of a mutation at one or both of the the restriction enzyme recognition sites. The locus metadata supplied by DArT has callrate included, but the call rate will change when some individuals are removed from the dataset. This script recalculates the callrate and places these recalculated values in the appropriate place in the genlight object. It sets the Call Rate flag to TRUE.
utils.recalc.callrate(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.avgpic for recalculating avgPIC,
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.callrate(testset.gl)
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