Admin: Hervé Pagès
Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès
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Comment:
C: BSgenome package building
... Yep. And don't fix the DESCRIPTION file. Fix the seed file instead and re-generate the package with forgeBSgenomeDataPkg("path/to/my/seed"). Also show us your seed file if things are still not working. Thanks!
...
written 6 days ago by
Hervé Pagès ♦♦ 13k
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... Hi Karl,
The issue with the 1st file (Trinity_kmer10.gff3.gz) is that it contains start/end values greater than 2^31-1. The problem was that, because these values cannot be stored in an R integer vector, makeTxDbFromGFF() was silently coercing them to NAs. I committed a change to rtracklayer (versi ...
written 7 days ago by
Hervé Pagès ♦♦ 13k
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... Hi,
Some very basic programming concepts are the notion of value, class, and variable.
A call like Biostrings::readDNAStringSet("wheatreference.fasta") returns a value (in this particular case the value is a DNAStringSet instance i.e. an object of class DNAStringSet). If you don't store this value ...
written 8 days ago by
Hervé Pagès ♦♦ 13k
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... round(cov) with some number of digits is a good option.
FWIW cov[cov < 0] <- 0 is slow because of the way x[i] <- value is currently implemented on Rle objects. The [<- method for Rle objects needs to be optimized. However, note that in the particular case of cov[cov < 0] <- 0, a ...
written 13 days ago by
Hervé Pagès ♦♦ 13k
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Answer:
A: Build GPos from IPos
... This is another reasonable feature request. Also added to the TODO list: https://github.com/Bioconductor/GenomicRanges/issues/13
Thanks,
H.
...
written 15 days ago by
Hervé Pagès ♦♦ 13k
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... Most of these transformations could indeed be supported on GPos objects. The intra-range transformations (shift, narrow, resize, flank, promoters, reflect, restrict, and trim) are generally expected to behave like endomorphisms (i.e. return an object of the same class as the input) so we would need ...
written 15 days ago by
Hervé Pagès ♦♦ 13k
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... Hi Thomas,
Please note that GRanges objects were never intended to support unlist(). However it used to be that unlist() would work on them, just by chance, and be a no-op. Not sure why your code calls unlist() on a GRanges object or what you expected it to do. What has changed in BioC 3.7 is that ...
written 28 days ago by
Hervé Pagès ♦♦ 13k
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... Hi Patrick,
It depends on the stranded protocol that was used to generate your paired-end RNA-seq data.
But first (and before I get to the details): Since I posted my original answer to this thread 3.5 years ago, 3 important functionalities have been added to the GenomicAlignments package:
GAli ...
written 5 weeks ago by
Hervé Pagès ♦♦ 13k
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... Hi,
Load the genomic coordinates of your fragments with rtracklayer::import(), use the object returned by rtracklayer::import() to extract the corresponding DNA sequences from the BSgenome object for mm9, then write the sequences to a FASTA file with Biostrings::writeXStringSet(). Will look somethi ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
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... So how would you like the output to look like? Can you forge the output "by hand" (for input gr2 and gr1) and show it here so I can see/understand what you would expect this enhanced subsetByOverlaps() to return?
Note that GRanges objects are not particularly good/convenient for representing one-to ...
written 7 weeks ago by
Hervé Pagès ♦♦ 13k
Latest awards to Hervé Pagès
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For A: Extracting Coordinates of startcodon from Grangeslist
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For A: coverage() output SimpleRleList cannot be converted to GRanges
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For A: Extracting Coordinates of startcodon from Grangeslist
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For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
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For A: coverage() output SimpleRleList cannot be converted to GRanges
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For A: Extracting Coordinates of startcodon from Grangeslist
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15 months ago,
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For A: Extracting Coordinates of startcodon from Grangeslist
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For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
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For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
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For A: Extracting Coordinates of startcodon from Grangeslist
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For A: overlapsAny for elements in GRangesList
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For A: How do I merge a list of GRanges?
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For A: about setdiff() and meta-information in GRanges
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For A: extract subsequence(s) from DNAStringSet with getSeq
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15 months ago,
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For A: coverage() output SimpleRleList cannot be converted to GRanges
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15 months ago,
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For unique, duplicated, order, etc... on a GRanges object
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For A: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
Scholar
15 months ago,
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For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
Scholar
15 months ago,
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For A: about setdiff() and meta-information in GRanges
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15 months ago,
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For A: extract subsequence(s) from DNAStringSet with getSeq
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15 months ago,
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For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
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For A: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
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For A: Error when running "locateVariants" function in "VariantAnnotation" package
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For A: A bug of "seqlevels<-" on TxDb
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For A: subsetByOverlaps with Multimapping
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