User: gen

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gen30
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Posts by gen

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Comment: C: Add up RLEs that are in lists?
... Hi, somewhat of a tangent, but if you wanted to shift a numeric RLE unchanged to a certain position or by a certain amount how could you do it? The closest I can find is shiftApply which I believe lines two RLEs together? But it doesn't seem to work on an RLE in isolation.   ...
written 2.7 years ago by gen30
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Comment: C: Add up RLEs that are in lists?
... Hi, yeah I want to get a big RLE not a single value. the second option unfortunately seems to give integer overflow errors. rror in unlist(RleList(ExampleRLElist)) : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .Call2("Rle_constructor", values, leng ...
written 2.7 years ago by gen30
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Add up RLEs that are in lists?
... Hi, I previously asked about summing RLEs but I'm now curious about extending the concept to summing lists of RLEs of arbitrary lengths. It seems fairly simple but I haven't seen a way to do it outside of loops. Given something like... $uc001aaa.3 numeric-Rle of length 249250621 with 5 runs Len ...
rnaseq genomicfeatures rle written 2.7 years ago by gen30 • updated 2.7 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: Shrink or Expand RLE
... It appears to work! But there are a couple hiccups, mostly related to line runLength(r) <- length.out * runLength(r)   If I normalize to  a large value like 1Kb I have integer overflow error. Is keeping the normalization value (length.out) the only way to fix this? Depending on what RLEs I r ...
written 2.7 years ago by gen30
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Comment: C: Shrink or Expand RLE
... Basically I want to shrink or expand a coverage range and its reads along the x axis. In the ascii example plots I showed above the first range is compressed into 1/2 its size. In the second example plot it is expanded to twice its size. The motivation is that I have read sets for ranges of several ...
written 2.7 years ago by gen30
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Comment: C: summing integer RLE
... cool it works for individual RLEs. I might need to do something with lists though. ...
written 2.7 years ago by gen30
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Shrink or Expand RLE
... If you have an RLE like this... integer-Rle of length 1575 with 42 runs Lengths: 982 1 1 2 3 2 ... 1 1 3 1 531 Values : 1 3 4 7 9 11 ... 8 6 5 3 1   how could you compress or expand the RLE along the x axis so the resulting graph compresses or expands a ...
coverage iranges granges rle written 2.7 years ago by gen30 • updated 2.7 years ago by Martin Morgan ♦♦ 21k
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Comment: C: summing integer RLE
... Hi, thanks but the answer collapses the RLE into one number. I need to find the average RLE in an RLElist. IE for two sets of coverage data. Combine them into one set and then average it out for mean coverage.   thanks ...
written 2.7 years ago by gen30
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summing integer RLE
... Hi,   Say you have something like this RleListexample RleList of length 4 $seq1 integer-Rle of length 1575 with 42 runs Lengths: 982 1 1 2 3 2 2 1 1 1 ... 1 1 1 2 1 1 3 1 531 Values : 0 2 3 6 8 10 12 13 15 17 ... 12 11 10 8 7 5 4 ...
grangeslist rle list irange written 2.7 years ago by gen30 • updated 2.7 years ago by Chris Seidel50
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Comment: C: Mean Coverage version of stat_coverage and coverage?
... If there is no equivalent to stat_coverage or coverage that can average several inputs. Would it be possible to possible to maybe 'average' the GRangeLists themselves? IE put them in equal sized bins and then for each position count how many reads cover that position and then divide it by the number ...
written 2.7 years ago by gen30

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