Simple quantifySNPs function. — quantifySNPs • ANTsR

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

Author

Avants BB

Examples


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