correctFUNHMM {MPR} | R Documentation |
~~ A concise (1-5 lines) description of what the function does. ~~
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), ...)
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~~ |
~~ If necessary, more details than the description above ~~
~Describe the value returned If it is a LIST, use
comp1 |
Description of 'comp1' |
comp2 |
Description of 'comp2' |
...
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~~further notes~~
~Make other sections like Warning with section{Warning }{....} ~
~~who you are~~
~put references to the literature/web site here ~
~~objects to See Also as help
, ~~~
##---- 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 }