Calculate a genome-wide estimate of Tajima's D, and optionally use simulation from the neutral model to correct for bias due to a minor-allele-frequency filter and perform a significance test.
1 2 |
object |
an object of class "vcfLink" |
maf |
the minimum allele frequency allowed in the null model simulations, as a proportion; SNPs with frequency < MAF are excluded from the simulations. The data is also thinned using this criterion prior to calculating D. |
nboot |
the number of bootstrap replicates used to generate a confidence interval around D; if 0, no bootstrap is performed |
nsim |
the number of simulations from the null model, used to correct bias due to the MAF and to test the significance of D; if 0, no correction is performed |
ploidy |
the ploidy of the organism |
use_vcftools_D |
if TRUE, use the method for calculating D implemented in vcftools, which is biased when there is missing data. If FALSE (default), use an unbiased (and faster) method |
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