User: Nicolas Servant

gravatar for Nicolas Servant
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Posts by Nicolas Servant

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Gene Density computation in pca.hic
... Hi Cath, Indeed, the gene density is calculated as  the number of genes falling in A (resp. B) compartments. Therefore as a sum. Would you have any reference explaining why using a mean might be better ? Best   ...
written 11 days ago by Nicolas Servant220
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Answer: A: HiTC importC not working
... Great ! Thanks. Nicolas ...
written 3 months ago by Nicolas Servant220
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Answer: A: HiTC importC not working
... Thanks. It looks good. I think the error occur on the xgi object. Did you check if your have intervals with negative widths ? The importC function is a small function. Could you try to excecute it line by line to see where exactly it crashed ... or at least ; xgi <- rtracklayer::import(xgi.b ...
written 3 months ago by Nicolas Servant220
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Answer: A: HiTC importC not working
... Hi, Indeed, it looks like the file was read, but that the parsing failed when it tries to create the GenomicRanges object (negatives widths). I'm wondering if the file could be corrupted by Windows character for instance ? Could you try ; xgi <- rtracklayer::import(xgi.bed, format = "bed") x ...
written 3 months ago by Nicolas Servant220
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Answer: A: normLGF yields non-symetric matrices
... thank you very much for your suggestion ! I will try to update the package for next release. Best ...
written 14 months ago by Nicolas Servant220
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Answer: A: normLGF yields non-symetric matrices
... Indeed ! I also checked in the original code from Hu et al. 2012, and this is the same. http://www.people.fas.harvard.edu/~junliu/HiCNorm/ So I agree that the matrix is no longer symmetric but the normalized values in i,j and j,i remains very close .. so I do not think that this is a real issue. ...
written 14 months ago by Nicolas Servant220
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Answer: A: normLGF yields non-symetric matrices
... Hi, Not sure to see why this lead to non-symmetrical matrices ? But indeed, this is not expected. Normalized matrices should also be symmetric. Best ...
written 14 months ago by Nicolas Servant220
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Answer: A: Is there a way to align Hi-C half heatmaps to Gviz track?
... Hi Nicolas, I would first advice you to have a look at the HiTC package which should help you handling such data. With HiTC, you should be able to plot your map and to add a track. However, the peaks will be interpreted as bars (i.e. start/end) below your maps ... so you will not have nice peaks. O ...
written 2.2 years ago by Nicolas Servant220
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Answer: A: FourC object from scratch
... Thank you Felix. It works. If useful, I can send you the function I wrote to build a FourC object from a BED file. Last question, when I apply the code from the vignette, I have no significant interaction, although I can see on the viewpoint plot some points higher than the dotted blue line (in bot ...
written 2.5 years ago by Nicolas Servant220
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Comment: C: FourC object from scratch
... might be useful ... > fragData GRanges object with 3999 ranges and 11 metadata columns:          seqnames                 ranges strand   |        name  leftSize             <Rle>              <IRanges>  <Rle>   | <character> <numeric>      [1]     chrX     [6062965 ...
written 2.5 years ago by Nicolas Servant220

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Popular Question 14 months ago, created a question with more than 1,000 views. For SAM and qvalue

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