Nothing
convert.variants.to.numeric <-
function(variants) {
type = attr(variants, "type")
# Strip off the header before making the conversion.
hdr = variants[,1:5]
variants = as.matrix(variants[,-1:-5])
# If there are confidence values, strip them out.
variants = strip.quality.columns(variants)
col.names = colnames(variants)
# Save the NA cells.
na.cells = which(is.na(variants))
# See which SNPs are equal to the reference allele.
# NOTE: if the SNPs is not bimorphic, this will make it bimorphic.
if(type == "snp") {
variants = variants == paste(hdr$REF, hdr$REF, sep = "")
} else if(type == "indel") {
variants = variants == paste(hdr$REF, hdr$REF, sep = "/")
} else if(type == "sv") {
variants = variants == "0"
} # else if(type == "sv")
# Make the SNPs a numeric matrix.
variants = matrix(as.numeric(variants), nrow(variants), ncol(variants),
dimnames = dimnames(variants))
# Replace the NA cells with NAs.
variants[na.cells] = NA
variants = data.frame(hdr, variants, stringsAsFactors = FALSE)
colnames(variants) = c(colnames(hdr), col.names)
attr(variants, "type") = type
return(variants)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.