correctFUNHMM {MPR}R Documentation

~~function to do ... ~~

Description

~~ A concise (1-5 lines) description of what the function does. ~~

Usage

correctFUNHMM(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), ...)

Arguments

x ~~Describe x here~~
base.position ~~Describe base.position here~~
hmmFUN ~~Describe hmmFUN here~~
geno.probability ~~Describe geno.probability here~~
transitionFUN ~~Describe transitionFUN here~~
emissionFUN ~~Describe emissionFUN here~~
... ~~Describe ... here~~

Details

~~ If necessary, more details than the description above ~~

Value

~Describe the value returned If it is a LIST, use

comp1 Description of 'comp1'
comp2 Description of 'comp2'

...

Warning

....

Note

~~further notes~~

~Make other sections like Warning with section{Warning }{....} ~

Author(s)

~~who you are~~

References

~put references to the literature/web site here ~

See Also

~~objects to See Also as help, ~~~

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--    or do  help(data=index)  for the standard data sets.

## The function is currently defined as
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), 
    ...) 
{
    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
  }

[Package MPR version 0.1 Index]