R/correctFUNHMM.R

correctFUNHMM <-
function (x, base.position = as.numeric(sub("[^0-9]*([0-9]*)[^0-9]*", 
                                              "\\1", names(x))), hmmFUN = hmm.vitFUN.rils, geno.probability = c(0.495, 
                                                                                                                0.495, 0.01), transitionFUN = phy2get.haldane.rils, emissionFUN = makeEmissionFUN(errorRate = 0.01), 
            ...) 
  {
    MPR_hetero_ = 0.5
    x.cr <- hmmFUN(geno = x + 1, position = base.position, geno.probability = geno.probability, 
                   transitionFUN = transitionFUN, emissionFUN = emissionFUN, 
                   ...) - 1
    x.cr[x.cr == 2] <- MPR_hetero_
    x.cr
  }

Try the MPR.genotyping package in your browser

Any scripts or data that you put into this service are public.

MPR.genotyping documentation built on May 2, 2019, 3:26 a.m.