I have found the htSeqTools methods useful for creating PCA plots of samples.  The filtering of reads to remove those that are deemed to be over amplified looks very interesting.

The function is called like this:
# BAM to IRanges object:
reads01 <- readAligned(dirPath , "reads01.bam", type='BAM')

ranges01 <- RangedData(ranges=IRanges(position(reads01),position(reads01)+width(reads01)), space=chromosome(reads01), strand=strand(reads01))

ranges01Fil <- filterDuplReads(ranges01, fdrOverAmp=0.01)

However, how can i get the filtered reads (ranges01Fil) out as BED formatted files?

Thank you!
Ian

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