getFws: Compute Fws within-host diversity statistic

In bahlolab/moimix: Estimating mulitplicity of infection from high-throughput sequencing data

Description

Compute Fws within-host diversity statistic

Usage

getFws(gdsfile)

Arguments

gdsfile

a SeqVarGDSClass object

Details

Compute the within host diversity statistic according to the method devised in Manske et.al, 2012. Briefly, within sample heterozygosity and within population heterozygosity are computed and assigned to ten equal sized MAF bins [0.0.05]...[0.45,0.5]. For each bin the mean within sample and population heterozygosity is computed. A regression line of these values through the orgin is computed for each sample. The Fws is then 1 - β.

Note

Currently only works on GATK derived gdsfiles. Needs to be updated to define populations.

References

Manske, Magnus, et al. "Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing." Nature 487.7407 (2012): 375-379.

See Also

getHeterozygosity, getHeterozygosityBySample

bahlolab/moimix documentation built on April 16, 2020, 8:40 a.m.