Export Noise Plot data

[hannesbecher]

Is there a way to export the noise plot data as CSV or similar? This would be most useful if one wanted to plot together and compare multiple datasets (like in the 2014 paper) without having to read in all BAM files again.

I tried to create a noise plot by hand starting with the filtered and corrected read counts readCountsCor:

avgReads <- apply(readCountsCor@assayData$counts, 2, mean)
vars <- apply(readCountsCor@assayData$counts, 2, function(x) matrixStats::varDiff(x/mean(x), trim=0.01))
snams <- unname(sapply(colnames(readCountsCor@assayData$counts), function(x) strsplit(x, "_")[[1]][[1]])) # specific to my file names
myNoiseData <- data.frame(snams, avgReads, vars)
write.table(myNoiseData, "myNoiseDataDown1Read.tsv", sep="\t", col.names=T, row.names=F, quote=F)

But the dot positions are not quite the same as in the actual plot. I presume the difference is that my code does not exclude blacklisted bins etc.

Is there a way to output the coordinates underlying the Noise Plot?

Many thanks,
Hannes