[BioC] "Normalising" GRanges coverage object
Aliaksei Holik
salvador at bio.bsu.by
Fri Aug 8 19:19:39 CEST 2014
Dear Bioconductors and especially *Ranges team,
I would like your expert opinion on whether what I'm doing is a sensible
thing to do.
I wish to plot some ChIP read coverage data in Gviz. The way I do it is
by reading a number of bam files with readGAlignments() and calculating
the coverage with the likewise named function. I would also like to
normalise the coverage for each bam file for library size and the Input
sample. I do so by simply dividing the coverage objects by the
respective library size and by the coverage object for the Input sample.
It all works beautifully, and the graphs look ok. But I'm left with a
nagging feeling, that it's too easy to be true. So I guess my question
is: am I right to assume that by dividing one coverage object by
another, the coverage at each position in one object would be divided by
the coverage at the same very position in the other object. I'm almost
expecting something to go wrong, if, for instance, I have 0 coverage at
some position in my reference object. But perhaps I should have faith in
Bioconductor.
Many thanks,
Aliaksei.
More information about the Bioconductor
mailing list