Nothing
summary.list<-function(object, Samples, threshold, length.base, chr=c(1:22,"X","Y"), ...)
{
labelSamples<-names(object)
Samples<-length(labelSamples)
if (missing(length.base))
{
warning("All segments are reported. If you want to filter the minimum and maximum \n lenght of segments, adjust 'length.base' \n (e.g. length.base=c(500,10e6) in base units)")
length.base<-c(0,Inf)
}
if (missing(threshold))
{
threshold<-c(NA,NA)
if(any(is.na(threshold)))
stop("Normal Limits cannot be estimated. Give 'threshold' argument manually")
}
ff<-function(x,chr,threshold,length.base)
{
cond<-x[,5]==chr & x[,6]!=0 & (x[,4]<threshold[1] | x[,4]>threshold[2]) & x[,2]-x[,1]>=length.base[1] & x[,2]-x[,1]<=length.base[2] & x[,2]-x[,1]>0
return(x[cond,])
}
ff2<-function(x,chr,threshold,length.base)
{
cond<-x[,5]==chr & x[,6]!=0 & x[,2]-x[,1]>0
xx<-x[cond,]
cond2<- (xx[,4]<=threshold[1] | xx[,4]>=threshold[2]) & xx[,2]-xx[,1]>=length.base[1] & xx[,2]-xx[,1]<=length.base[2]
return(!cond2)
}
ans<-list()
no.cnv<-list()
for (i in 1:length(chr))
{
ans[[i]] <-lapply(object, FUN=ff, chr=chr[i], threshold=threshold, length.base=length.base)
no.cnv[[i]] <-lapply(object, FUN=ff2, chr=chr[i], threshold=threshold, length.base=length.base)
}
attr(ans,"no.cnv")<-no.cnv
attr(ans,"length.base")<-length.base
attr(ans,"threshold")<-threshold
attr(ans,"Info")<-object
attr(ans,"Samples")<-c(1,Samples)
attr(ans,"labels.samples")<-labelSamples
attr(ans,"chr")<-chr
class(ans)<-"summaryParGADA"
names(ans)<-paste("chromosome",chr)
ans
}
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.