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cross2gpData <- function(cross) {
# check for class
# sometimes multiple classes in package 'qtl'
if (all(class(cross) != "cross")) stop("object '", substitute(cross), "' not of class 'cross'")
# phenotypic data
pheno <- cross$pheno
# names of chromosomes
chr <- names(cross$geno)
# extract information from first chromosome
geno <- cross$geno[[chr[1]]]$data
map <- data.frame(chr = chr[1], pos = cross$geno[[chr[1]]]$map)
# loop over chromosomes 2:n
if (length(chr) > 1) {
for (i in chr[-1]) {
# add new genotypes
geno <- cbind(geno, cross$geno[[i]]$data)
# add new map info
map <- rbind(map, data.frame(chr = i, pos = cross$geno[[i]]$map))
}
}
# combine pheno, geno, and map in class 'gpData'
ret <- create.gpData(pheno = pheno, geno = geno, map = map)
# recode
# coding in cross: 1 = AA, 2 = AB, 3 = BB,
ret$geno <- ret$geno - 1
return(ret)
}
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