User: Ludo Pagie

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Ludo Pagie40
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40
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New User
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Last seen:
3 years, 8 months ago
Joined:
6 years, 2 months ago
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l*********@gmail.com

Posts by Ludo Pagie

<prev • 5 results • page 1 of 1 • next >
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width(GRanges) increases after randomizeRegions(..) in package RegioneR
... Hi all, I want to compare overlap of 2 sets of genomic features to a case where one set is randomly distributed over the genome. For this I'm using the function randomizeRegions(..) in the package regioneR. The width of the randomized regions is 1 longer than the width of the input regions. Indeed ...
genomicranges regioner width written 3.8 years ago by Ludo Pagie40 • updated 3.8 years ago by bernatgel120
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Creating DataFrame uses too much memory
... Dear all, I know I'm on slippery slopes here with stating some R-feature uses too much memory. Still I find something odd which hampers me in getting my job done. I make a DataFrame from a large integer matrix (rowaxcols = 7e6 x 300) and the process of creating the DataFrame consumes more memory th ...
cancer process written 5.4 years ago by Ludo Pagie40 • updated 5.4 years ago by Michael Lawrence11k
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DataFrame(..., check.names=F); colnames change when assign data using '[[', not when using '[,]'
... Dear all, I'm using GRanges objects ('df') to store read counts on 7M genomic regions. I found that the colnames of mcols(df) do not behave nicely when using the names are not 'syntactic valid'. But this behavior depends on whether columns are referenced using '[[' or using '['. I would think this ...
assign written 5.5 years ago by Ludo Pagie40 • updated 5.5 years ago by Michael Lawrence11k
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error when coercing GenomeData to RangedData: 'no method or default for coercing “XStringViews” to “RangedData”'
... Hi all, I'm getting an error when trying to coerce a GenomeData object to a RangedData object. Here's the code I have used together with some output (in particular the error msg when coercing): ###################################################################### # import human genome sequence l ...
bsgenome written 5.5 years ago by Ludo Pagie40 • updated 5.5 years ago by Michael Lawrence11k
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coverage() in IRanges gives >0 coverage when weight == 0
... Hi all, I don't understand what's going on here.I'm trying to compute the coverage of a few ranges. I specify a weight for these ranges and for some positions I get a coverage even though I know these positions are only covered by ranges which have 0 weight. Worse, the value I do get for these posi ...
coverage written 6.2 years ago by Ludo Pagie40 • updated 6.2 years ago by Charles Berry290

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For Creating DataFrame uses too much memory

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