Admin: Hervé Pagès
Hervé Pagès ♦♦ 12k
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Posts by Hervé Pagès
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... Hi,
I would need to be able to reproduce this error in order to troubleshoot. Do you think you can make your BAM file available somewhere? Or a subset of it only as long as it allows me to reproduce the error. Thanks!
H.
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written 4 days ago by
Hervé Pagès ♦♦ 12k
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... Hi D.,
If there is no OrgDb package for your non model organism, and you need one, then I guess you'd want to make one. Not clear to me why you'd want to put these annotations in a BSgenome data package. These packages are meant for the genome sequences. Could you clarify what you are trying to do? ...
written 4 days ago by
Hervé Pagès ♦♦ 12k
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Comment:
C: reduce function in GenomicRanges
... Oh I see now why you expected ranges chr1:5-10 and chr1:95-101 to be merged. Sorry for missing that. I modified my answer above to support the min.gapwidth argument. Also fixed a bug in circularReduceIRanges().
Cheers,
H.
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written 4 days ago by
Hervé Pagès ♦♦ 12k
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... [Edited on Jul 23, 2017: Simplified and fixed bug in circularReduceIRanges(). Also added the min.gapwidth argument.]
Hi,
Indeed, reduce() does not handle circularity yet.
The circularReduceGRanges() function below implements a circularity-aware reduction for GRanges objects:
seqinfo <- Seqin ...
written 6 days ago by
Hervé Pagès ♦♦ 12k
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Comment:
C: CAGEr BAM files size issue
... Hi,
You're using the CAGEr package so I'm not sure exactly how the Biostrings package could help you solve this issue. Unless I add support for long XString objects, which is on the radar but unlikely to happen in the near future. In the mean time, one way to solve the issue would be to revisit the ...
written 6 days ago by
Hervé Pagès ♦♦ 12k
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Comment:
C: CAGEr BAM files size issue
... Hi,
The error message is coming from Biostrings and is admittedly not helpful. I just changed this in Biostrings 2.44.2 and now it says:
> unlist(big_dna_string_set)
Error in .Call2("XStringSet_unlist", x, PACKAGE = "Biostrings") :
XStringSet object is too big to be unlisted (would result i ...
written 7 days ago by
Hervé Pagès ♦♦ 12k
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... Hi,
Something looks wrong with your GTF file. Do you think you can make it available somewhere so we can look at it? Thanks,
H.
...
written 7 days ago by
Hervé Pagès ♦♦ 12k
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... By wrapping the call generating the warning inside suppressWarnings(). This is the standard way to suppress warnings in R. See ?suppressWarnings for more information.
Cheers,
H.
...
written 8 days ago by
Hervé Pagès ♦♦ 12k
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... Hi,
Michael replaced the ifelse generic and methods with a new ifelse2 generic and methods in IRanges 2.11.8. So AFAICT no Bioconductor package defines any ifelse method anymore.
Cheers,
H.
...
written 9 days ago by
Hervé Pagès ♦♦ 12k
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535
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... Hi,
The little findTandemRepeats() function I provided above is designed to work on a DNAString object so all you need to do is load the Biostrings package and turn your raw sequence into a DNAString object before calling findTandemRepeats on it:
library(Biostrings)
findTandemRepeats(DNAString("A ...
written 9 days ago by
Hervé Pagès ♦♦ 12k
Latest awards to Hervé Pagès
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: How do I merge a list of GRanges?
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Scholar
3 months ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
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Teacher
3 months ago,
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For A: How do I merge a list of GRanges?
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3 months ago,
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For A: A bug of "seqlevels<-" on TxDb
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For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
Teacher
5 months ago,
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For A: How do I merge a list of GRanges?
Scholar
5 months ago,
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For A: A bug of "seqlevels<-" on TxDb
Scholar
5 months ago,
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For A: A bug of "seqlevels<-" on TxDb
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15 months ago,
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For A: XStringSet operations discard names - how to address?
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For A: kmer and zscore calculation
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15 months ago,
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For A: XStringSet operations discard names - how to address?
Teacher
15 months ago,
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For A: pairwiseAlignments coordinate mapping?
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For A: pairwiseAlignments coordinate mapping?
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For A: vcountPattern for Pattern Contained within or Containing Subject
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For A: how much positions overlapped for each pair of the pairs obtained by findover
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For A: makeTxDbFromUCSC fails to download refLink table
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For A: Generating a proper TxDb instance from NCBI GFF Annotations File
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For A: overlapsAny for elements in GRangesList
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