Simple quantifySNPs function.

quantifySNPs converts trinary snps to frequency data

quantifySNPs(
  snps,
  freqthresh = 0.1,
  shiftit = FALSE,
  replaceWithF = TRUE,
  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)
#> 
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