User: Nicolas Servant

gravatar for Nicolas Servant
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Posts by Nicolas Servant

<prev • 31 results • page 1 of 4 • next >
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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 7 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 7 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 7 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 19 months 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 23 months 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 24 months ago by Nicolas Servant220
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Answer: A: FourC object from scratch
... Still an issue with getDistAroundVp from getZScores Error in mcols(mcols(fragData))[colnames(mcols(fragData)) %in% newCols,  :   type / longueur incorrect (S4 / 0) It seems that mcols(mcols(fragData)) is NULL in my case ? Did I miss something ? Thank you again Nicolas   ...
written 24 months ago by Nicolas Servant220
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Answer: A: FourC object from scratch
... ok. Thank you Felix. I will try it. ...
written 24 months ago by Nicolas Servant220
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Answer: A: FourC object from scratch
... Hi Felix, Still trying to adapt FourCSeq to other 'C' data. I build my FourC object from scratch, with many empty fields following our previous discussion. Then when I used the getZScores, it crashed because leftSize, rightSize, leftValid, rightValid are not defined. The line fragData$blind = fra ...
written 24 months ago by Nicolas Servant220
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FourC object from scratch
... Hi Felix, You're rigth, I move to the BioC list. I tried your exemple, it works well. In the exptData, do I really need all these fields ? or can I use an empty string for projectPath, fragmentDir, reSequence1 ... ? Then, just to clarify some points ; fc@colData is your experimental design, so ...
hitc fourcseq hi-c written 2.1 years ago by Nicolas Servant220

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