User: Assa Yeroslaviz

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Assa Yeroslaviz1.3k
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Posts by Assa Yeroslaviz

<prev • 252 results • page 2 of 26 • next >
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Comment: C: (Big)wig file of complete chromosome
... yes thanks, I have figured it out by now. I am using now the rep() command instead.  ...
written 21 days ago by Assa Yeroslaviz1.3k
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subsetting GRanges object based on gene IDs
... Hi, I have a GRanges object e.g. GRanges object with 6 ranges and 1 metadata column:            seqnames         ranges strand |     gene_id               <Rle>      <IRanges>  <Rle> | <character>   15S_rRNA       MT [ 6546,  8194]      + |    15S_rRNA   21S_rRNA       MT [ ...
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Comment: C: (Big)wig file of complete chromosome
... after trying this example and not understanding, why it doesn't do what I want, I figured it out. The Rle() options looks better, but if I use it, I can't export the data as bedgraph (or bigwig). I get an error message claiming Scores must be non-NA numeric values.  Is there a way to coerce the Rl ...
written 21 days ago by Assa Yeroslaviz1.3k
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Comment: C: (Big)wig file of complete chromosome
... But what if I'm using t he Ensembl annotations? so my chromosome names differs from the standard UCSC naming? ...
written 4 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: (Big)wig file of complete chromosome
... Thanks, this I know. I thought there might be a better way. ...
written 4 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: (Big)wig file of complete chromosome
... Thanks, this looks very nice. I will try it. I have a question though. I am familiar with the seqlengths when creating a GRanges object. But here I am reading a bedgraph file into R. How do I give the import.bw or import.bedgraph the seqlength() parameter?  ...
written 4 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: (Big)wig file of complete chromosome
... thanks for the suggestion, but it is still not exactly what i need. The code above doesn't take the ends of each chromosome into account. This leads to different number of entries in the two GRanges objects. e.g. > InputIP.control[seqnames(InputIP.control) == "I"] GRanges object with 92413 rang ...
written 5 weeks ago by Assa Yeroslaviz1.3k
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Comment: C: (Big)wig file of complete chromosome
... Thanks Michael for the neat solution. it is still not what i need though. The coverage function summarize the similar values into one row like that: GRanges object with 5793227 ranges and 1 metadata column: seqnames ranges strand | score <Rle> < ...
written 6 weeks ago by Assa Yeroslaviz1.3k
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(Big)wig file of complete chromosome
... Hi,   I have a list of bigwig files from different data sets. We would like to create a table of all the genomic positions per chromosome to be able to compare the samples with each other.  As the peaks found in each samples are at different chromosomal positions, I would like to complete each ch ...
rtracklayer granges grangeslist bigwig import written 7 weeks ago by Assa Yeroslaviz1.3k • updated 7 weeks ago by Michael Lawrence9.6k
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'memory not mapped' error when running monocole
... Hi, when trying to analyse time-sereis analysis of single-cells RNASeq with monocole, my R session crashes, when I try to get the structure of my CellDataSet object.  This is the script I am using ( it is a minimal example I created for the reproduction of the error message): library(monocle) li ...
monocole memory celldataset written 4 months ago by Assa Yeroslaviz1.3k

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Appreciated 5 months ago, created a post with more than 5 votes. For A: Problem with biomart's listMarts function
Popular Question 5 months ago, created a question with more than 1,000 views. For extract intensity values from AffyBatch
Popular Question 7 months ago, created a question with more than 1,000 views. For DESeq2 produces adjusted p-values = 1
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Popular Question 17 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Problem with biomart's listMarts function
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Popular Question 23 months ago, created a question with more than 1,000 views. For could not find symbol "keepNA" in environment of the generic function
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