Entering edit mode
Marcin Imielinski
▴
30
@marcin-imielinski-5383
Last seen 10.2 years ago
Hi,
I'm using rtracklayer with RangedData and Rle to analyze numerical
tracks
from wig and bigwig files.
Ideally I'd like to convert the RangedData that comes from import.bw
into
Rle format; however, the only way to do this (quickly) appears to be
the
IRanges function coverage(x, weight = 'score'), where x is a
RangedData
object.
The problem is that coverage() only accepts integer weights. This
works
fine for integer tracks (e.g. counts) but does not readily work
RangedData
with a floating point "score".
My interim solution for non-integer RangedData has been a hack: I
multiply
the score of the input RangedData by 10^(precision), run coverage, and
then
divide the Rle output by 10^(precision). This is an ok fix for now,
however in the long term could cause ugly rounding problems (eg for
tracks
with more than 8 log orders magnitude difference between the smallest
and
largest score +/- high degree of interval overlap).
Any suggestions for better approaches for dealing with this problem?
Session info below.
Thanks in advance,
Marcin
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)
[[alternative HTML version deleted]]