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List:       bioconductor
Subject:    [BioC]  htSeqTools - filtered reads > BED?
From:       Ian Donaldson <Ian.Donaldson () manchester ! ac ! uk>
Date:       2012-01-27 11:56:23
Message-ID: 7E756F18289AF64B967C333AC3BF7021C6728B70 () MBXP02 ! ds ! man ! ac ! uk
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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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