Admin: Hervé Pagès

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Hervé Pagès ♦♦ 11k
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Posts by Hervé Pagès

<prev • 1,396 results • page 1 of 140 • next >
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Answer: A: how to extract part of the DNA sequences from a DNAstringset
... Hi XIA, You can use extractAt to extract the sequences corresponding to the hits: extractAt(sread, hits) See ?extractAt for more information. If you have off-limits hits, you can either get rid of them with: hits <- as(hits, "CompressedIRangesList") hits <- hits[start(hits) >= 1 & ...
written 4 hours ago by Hervé Pagès ♦♦ 11k
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Answer: A: How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scal
... Hi Ramiro, FWIW I recently made a SNPlocs package for dbSNP Build 149 (the latest dbSNP build) but it's only available in BioC devel (i.e. BioC 3.5, requires R 3.4): https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP149.GRCh38 I actually highly recommend that you upgrade your installation t ...
written 6 hours ago by Hervé Pagès ♦♦ 11k
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Answer: A: question about summrizeOverlaps
... Hi, Your own examples show that it does accept reads represented as a GRangesList object. So maybe you're wondering why you get a different result when you replace reads with reads$A? The GRangesList representation is interpreted as "one read per list element". For example, if an aligned read has ...
written 1 day ago by Hervé Pagès ♦♦ 11k
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Comment: C: GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
... Hi, Maybe the problem is that you're not using the latest released version of Bioconductor (which is 3.4). Some fixes were applied recently to makeTxDbFromBiomart() in BioC 3.4 (and in BioC devel) to work around some issues introduced by some changes on the Ensembl Mart side. Try to load the BiocI ...
written 7 days ago by Hervé Pagès ♦♦ 11k
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Answer: A: IRanges object from count matrix
... Hi Assa, Looks like you have a data.frame, not a matrix. You can call makeGRangesFromDataFrame() on it to turn it into a GRanges object. You might want to call the function with keep.extra.columns=TRUE to preserve the Length column. See ?makeGRangesFromDataFrame for the details. Note that the star ...
written 7 days ago by Hervé Pagès ♦♦ 11k
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Comment: C: how to renameSeqlevels-GenomicAlignments
... If by "bam file mapped on transcript" you mean that your reads have been aligned to the transcriptome, then you need to realize that the positions in your BAM file (and therefore in your GAlignments object) are relative to the transcriptome. OTOH GFF files annotate genomic features with respect to t ...
written 8 days ago by Hervé Pagès ♦♦ 11k
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Answer: A: how to renameSeqlevels-GenomicAlignments
... Yes renameSeqlevels() should work but you have to call it on your GAlignments object, not on seqlevels(bamfile). Also I'm not sure what listx is in your code above and how you made it. Your description of what you did is confused. It is generally more useful to show the exact code you used, includin ...
written 8 days ago by Hervé Pagès ♦♦ 11k
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Comment: C: matching of AAStringSet vs. another AAStringSet
... Hi Tobi, I can't really give a detailed explanation because I don't have enough information about how you obtained m. It seems that you used vmatchPattern() in an lapply() loop so you ended up with a list of 1 MIndex object per peptide sequence. The memory footprint of an MIndex object is: s ...
written 8 days ago by Hervé Pagès ♦♦ 11k
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Comment: C: Printing DataFrame with nested DataFrames causes error
... Great, thanks! I should probably do the same for DelayedArray objects. H. ...
written 8 days ago by Hervé Pagès ♦♦ 11k
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Comment: C: Printing DataFrame with nested DataFrames causes error
... Thanks Michael. I forgot about df[[i, j]] (I never use it) but it works on ordinary data frames and does df[[j]][[i]]: df[4, 3] # [[1]] # data frame with 0 columns and 0 rows df[[4, 3]] # data frame with 0 columns and 0 rows Maybe DataFrame objects could support it too. H. ...
written 11 days ago by Hervé Pagès ♦♦ 11k

Latest awards to Hervé Pagès

Scholar 20 days ago, created an answer that has been accepted. For A: A bug of "seqlevels<-" on TxDb
Scholar 10 months ago, created an answer that has been accepted. For A: how much positions overlapped for each pair of the pairs obtained by findover
Scholar 10 months ago, created an answer that has been accepted. For A: Requesting flank sequences (BioMart::Exception)
Scholar 10 months ago, created an answer that has been accepted. For A: GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
Scholar 10 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Scholar 10 months ago, created an answer that has been accepted. For A: XStringSet operations discard names - how to address?
Scholar 10 months ago, created an answer that has been accepted. For A: matching of AAStringSet vs. another AAStringSet
Scholar 10 months ago, created an answer that has been accepted. For A: SNP extraction from SNPlocs.Hsapiens.dbSNP144.GRCh38
Scholar 10 months ago, created an answer that has been accepted. For A: a package for read.fasta
Scholar 10 months ago, created an answer that has been accepted. For A: Cannot load old SummarizedExperiment in R 3.3, Bioc 3.3
Scholar 10 months ago, created an answer that has been accepted. For A: pairwiseAlignments coordinate mapping?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: pairwiseAlignments coordinate mapping?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: kmer and zscore calculation
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: XStringSet operations discard names - how to address?
Scholar 10 months ago, created an answer that has been accepted. For A: getting a directed and unweighted adjacency matrix with igraph package
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: how much positions overlapped for each pair of the pairs obtained by findover
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Memory-efficient method to calculate GC content of millions of GRanges
Scholar 10 months ago, created an answer that has been accepted. For A: problem with @ranges@start in DNAStringSet
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How do I merge a list of GRanges?
Scholar 10 months ago, created an answer that has been accepted. For A: resize (shrink/expand) GenomicRanges
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: overlapsAny for elements in GRangesList
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Generating a proper TxDb instance from NCBI GFF Annotations File
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromUCSC fails to download refLink table
Scholar 10 months ago, created an answer that has been accepted. For A: troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not fo
Scholar 10 months ago, created an answer that has been accepted. For A: Memory-efficient method to calculate GC content of millions of GRanges

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