correctGeno {MPR}R Documentation

~~function to do ... ~~

Description

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

Usage

correctGeno(geno.data, base.position = as.numeric(sub("[^0-9]*([0-9]*)[^0-9]*", "\1", rownames(geno.data))), correct.FUN = correctFUNHMM, minInterval = 1, verbose = TRUE, ...)

Arguments

geno.data ~~Describe geno.data here~~
base.position ~~Describe base.position here~~
correct.FUN ~~Describe correct.FUN here~~
minInterval ~~Describe minInterval here~~
verbose ~~Describe verbose 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 (geno.data, base.position = as.numeric(sub("[^0-9]*([0-9]*)[^0-9]*", 
    "\1", rownames(geno.data))), correct.FUN = correctFUNHMM, 
    minInterval = 1, verbose = TRUE, ...) 
{
    i <- 0
    geno.data.cr <- apply(geno.data, 2, function(x, ...) {
        if (verbose) 
            cat("\r", i <<- i + 1)
        x.nna <- which(!is.na(x))
        ids <- sort(unique(x.nna[c(1, which(diff(x[x.nna]) != 
            0 | diff(base.position[x.nna]) >= minInterval) + 
            1)]))
        x.cr <- correct.FUN(x[ids], base.position = base.position[ids], 
            ...)
        x[x.nna] <- NA
        x[ids] <- x.cr
        x
    }, ...)
    if (verbose) 
        cat("\tDone.\n")
    geno.data.cr
  }

[Package MPR version 0.1 Index]