Converting floating point RangedData to Rle
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@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]]
Coverage convert rtracklayer Coverage convert rtracklayer • 815 views
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