ANTsR (version 0.3.3)

quantifySNPs: Simple quantifySNPs function.

Description

quantifySNPs converts trinary snps to frequency data

Usage

quantifySNPs(snps, freqthresh = 0.1, shiftit = FALSE, replaceWithF = T, traitvecin = NA, trainvec = NA)

Arguments

snps

input matrix

freqthresh

remove snps below this frequency

shiftit

shift the snps to smooth the estimate

replaceWithF

replaces snps with frequency values

traitvecin

map snps to trait vector

trainvec

defines training data

Value

matrix is output

Examples

mat <- matrix(c(0,1,2,0,0,1,2,2,2),ncol=3)
wmat<-quantifySNPs( mat , freqthresh=0)