rCNV (version 1.3.0)

vst: Calculate population-wise Vst

Description

This function calculates Vst (variant fixation index) for populations given a list of duplicated loci

Usage

vst(AD, pops, id.list = NULL, qGraph = TRUE, verbose = TRUE, ...)

Value

Returns a matrix of pairwise Vst values for populations

Arguments

AD

data frame of total allele depth values of (duplicated, if id.list is not provided) SNPs

pops

character. A vector of population names for each individual. Must be the same length as the number of samples in AD

id.list

character. A vector of duplicated SNP IDs. Must match the IDs in the AD data frame

qGraph

logical. Plot the network plot based on Vst values (see details)

verbose

logical. show progress

...

additional arguments passed to qgraph

Author

Piyal Karunarathne

Details

Vst is calculated with the following equation $$V_{T} = \frac{ V_{S} }{V_{T}}$$ where VT is the variance of normalized read depths among all individuals from the two populations and VS is the average of the variance within each population, weighed for population size (see reference for more details) See qgraph help for details on qgraph output

References

Redon, Richard, et al. Global variation in copy number in the human genome. nature 444.7118 (2006)

Examples

if (FALSE) data(alleleINF)
data(ADtable)
DD<-dupGet(alleleINF)
ds<-DD[DD$dup.stat=="deviant",]
ad<-ADtable[match(paste0(ds$CHROM,".",ds$POS),paste0(ADtable$CHROM,".",ADtable$POS)),]
vst(ad,pops=substr(colnames(ad)[-c(1:4)],1,11))