Nothing
setupGADAIllumina <-
function(file, NumCols, log2ratioCol, MarkerIdCol=1, ChrNameCol=2, ChrPosCol=3, XY=TRUE, sort=TRUE, orderProbes, saveGenInfo=TRUE)
{
if (missing(log2ratioCol))
stop("Missing log2ratioCol. Please, indicate which column of the file contains the log2ratio")
if (missing(NumCols))
stop("Missing NumCols argument. Please, indicate the number of columns in the file")
ans<-list()
xx<-scan(file, skip=1, what=c("character"), sep="\t")
## Validating headers for the Illumina files
headers <- scan(file, nline=1, what=c("character"), quiet=TRUE, sep="\t")
if(headers[MarkerIdCol]!='Name')
warning("Expecting 'Name' as the header of MarkerIdCol in an Illumina file")
if(headers[ChrNameCol]!='Chr')
warning("Expecting 'Chr' as the header of ChrNameCol in an Illumina file")
if(!headers[ChrPosCol]%in%c('position', 'Position'))
warning("Expecting 'position' as the header of ChrPosCol in an Illumina file")
if(NROW(grep("Log.R.Ratio",headers[log2ratioCol]))!=1)
warning("Expecting 'Log R Ratio' as the header of log2ratioCol in an Illumina file")
x<-matrix(xx, ncol=NumCols, nrow=length(xx)/NumCols, byrow=TRUE)
if (!sort)
{
x[,ChrNameCol][x[,ChrNameCol]=="XY"]<-"X"
if (XY)
{
chr<-factor(x[,ChrNameCol],levels=c(as.character(1:22),"X","Y"))
}
else
{
x[,ChrNameCol][x[,ChrNameCol]=="23"]<-"X"
x[,ChrNameCol][x[,ChrNameCol]=="24"]<-"Y"
chr<-factor(x[,ChrNameCol],levels=c(as.character(1:22),"X","Y"))
}
temp<-data.frame(probe=x[,MarkerIdCol],chr=chr,pos=as.numeric(x[,ChrPosCol]),stringsAsFactors=FALSE)
# Mitocondrial (or missing)
mito<-is.na(temp$chr) | is.na(temp$pos)
temp2<-temp[!mito,]
ans$log.ratio<-as.numeric(x[!mito,log2ratioCol])
attr(ans,"gen.info")<-temp2
}
else # if sort
{
x[,ChrNameCol][x[,ChrNameCol]=="XY"]<-"X"
if (XY)
{
chr<-factor(x[,ChrNameCol],levels=c(as.character(1:22),"X","Y"))
}
else
{
x[,ChrNameCol][x[,ChrNameCol]=="23"]<-"X"
x[,ChrNameCol][x[,ChrNameCol]=="24"]<-"Y"
chr<-factor(x[,ChrNameCol],levels=c(as.character(1:22),"X","Y"))
}
pos<-as.numeric(x[, ChrPosCol])
if (missing(orderProbes))
o<-order(chr,pos)
else
o<-orderProbes
temp<-data.frame(probe=x[o,MarkerIdCol],chr=chr[o],pos=pos[o],stringsAsFactors=FALSE)
# Mitocondrial
mito<-is.na(temp$chr) | is.na(temp$pos)
temp2<-temp[!mito,]
aux<-as.numeric(x[o,log2ratioCol])
ans$log.ratio<-aux[!mito]
attr(ans,"gen.info")<-temp2
}
attr(ans,"type")<-"Illumina"
if (!saveGenInfo)
attr(ans, "gen.info")<-TRUE
class(ans)<-"setupGADA"
ans
}
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