Nothing
patchwork.createreference = function(...,output="REFOUT")
{
data=NULL
files = list(...)
data(ideogram,package="patchworkData")
chroms=as.character(unique(ideogram$chr))
j = 0
for (i in files)
{
j = j + 1
cat(paste("Reading Chromosomes of file ",i," \n",sep=""))
data[[j]] = patchwork.readChroms(i,chroms)
cat(paste("Initiating Gc Normalization of file ",i," \n",sep=""))
data[[j]] = patchwork.GCNorm(data[[j]])
data[[j]] = data[[j]][c("chr","pos",
#"counts",
"norm")]
}
if (j > 1)
{
cat("Merging the files into reference. \n")
data_ = merge(data[[1]],data[[2]],all=TRUE,by=1:2)
if (j > 2)
{
for (c in 3:j)
{
data_ = merge(data_,data[[c]],all=TRUE,by=1:2)
}
}
#counts_ = seq(from=3,to=(length(data_) - 1),by=2)
norm_ = seq(from=3,to=length(data_),by=1)
cat("Creating and applying mean functions to the reference. \n")
normaldata = data.frame(chr=data_$chr,pos=data_$pos,
#counts_mean=apply(data_[,counts_],
#1,mean,na.rm=TRUE),
reference=apply(data_[,norm_],
1,mean,na.rm=TRUE))
}
else
{
data = data[[j]]
cat("Creating and applying mean functions to the reference. \n")
cat("Note: Creating from single bamfile. Cannot obtain mean ")
cat("counts or norm however naming columns counts_mean and ")
cat("norm_mean for compatability \n")
normaldata = data.frame(chr=data$chr,pos=data$pos,#gc=data$gc,
#gck=data$gck,gcm=data$gcm,
#counts_mean=data$counts,
reference=data$norm)
}
#conform chromosome naming to suit
cat("Saving to ",output,".Rdata \n",sep="")
save(normaldata,file=paste(output,".Rdata",sep=""))
return(normaldata)
}
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