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Is There Software For Generating A Histogram Or Boxplot From Values In Bedgraph Files?

I was wondering if there was software to generate histograms of a set of input bedgraph files so that we could look at the output and compare the signals of the tracks. Our goal is to see if these values are comparable; that the data sets are of a similarity quality.

graphs
• 4,520 views • link
updated by Madelaine Gogol Madelaine Gogol • written by Paul • Paul

2 answers

Here's some R code:

library(rtracklayer)
setwd("mywigdir")
files<-Sys.glob("*.wig")
d<-list()
pdf("hists.pdf")
for( i in 1:length(files))
{
    d[[i]]<-import.wig(files[i])
    hist(d[[i]]$score,breaks=20,xlim=c(-6,6),col='blue')
}
dev.off()

Or you could make a boxplot of the scores:

scores<-lapply(d,function(x){x$score})
boxplot(scores,names=files,las=2,cex.axis=.6)
• 0 views • link
written by Madelaine Gogol Madelaine Gogol

Thank you. It turns out your solution is technically correct, unfortunately we are now running into the problem that our data sets are extremely large. The signal file itself is 2.5G which takes an unreasonable amount of RAM in R.

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written by Paul • Paul

Ah, you know, I was wondering about that... You could sample the file somehow ahead of time if you're only interested in the general distribution of scores...

• 0 views • link
written by Madelaine Gogol Madelaine Gogol

Anything that can generate histograms or box plots should do the job, such as R. In R, a simple "boxplot(y ~ group)" allows you to plot your data by a grouping factor "group".

• 0 views • link
written by Wen.Huang Wen.Huang

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