vstPermutation: Run permutation on Vst
In rCNV: Detect Copy Number Variants from SNPs Data

vstPermutation

R Documentation

Run permutation on Vst

Description

This function runs a permutation test on Vst calculation

Usage

vstPermutation(
  AD,
  pops,
  nperm = 100,
  histogram = TRUE,
  stat = 2,
  qGraph = TRUE
)

Arguments

`AD`	data frame of total allele depth values of SNPs
`pops`	character. A vector of population names for each individual. Must be the same length as the number of samples in AD
`nperm`	numeric. Number of permutations to perform
`histogram`	logical. plots the distribution histogram of permuted vst values vs. observed values
`stat`	numeric. The stat to be plotted in histogram. 1 for Mean Absolute Distance or 2 (`default`) for Root Mean Square Distance
`qGraph`	logical. Plot the network plot based on observed Vst values (see `vst()` help page for more details)

Value

Returns a list with observed vst values, an array of permuted vst values and the p-values for the permutation test

Author(s)

Jorge Cortés-Miranda (email:jorge.cortes.m@ug.uchile.cl), Piyal Karunarathne

Examples

## Not run: 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)),]
vstPermutation(ad,pops=substr(colnames(ad)[-c(1:4)],1,11))
## End(Not run)

rCNV documentation built on Sept. 30, 2024, 9:39 a.m.