Admin: Hervé Pagès
Hervé Pagès ♦♦ 14k
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- Joined:
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Posts by Hervé Pagès
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Answer:
A: vcountPDict fails on PDict
... Hi Aditya,
Maybe you were looking at the wrong man page. `vcountPDict()` is a generic function with dispatch on the 2nd argument (`subject`):
```
library(BSgenome)
vcountPDict
# standardGeneric for "vcountPDict" defined from package "Biostrings"
# function (pdict, subject, max.mismatch = 0, min.mi ...
written 5 days ago by
Hervé Pagès ♦♦ 14k
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... Hi Jiping,
`reduce()` is vectorized on a GRangesList object so there is no need to use `endoapply()`:
```
library(GenomicRanges)
grl <- GRangesList(GRanges(c("chr1:21-30", "chr1:28-35")),
GRanges(c("chr1:25-30", "chr1:35-40")),
GRanges(c("chr1:31-37", "chr1: ...
written 12 days ago by
Hervé Pagès ♦♦ 14k
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... Hi Jiping,
`coverage()` and family (including `coverageByTranscript()`) always turn a GAlignmentPairs object into a GRangesList object internally before computing the coverage. More precisely, if `x` is a GAlignmentPairs object, `coverage(x, ...)` and `coverageByTranscript(x, ...)` are equivalent t ...
written 15 days ago by
Hervé Pagès ♦♦ 14k
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... No it's not. As I said earlier, we don't have access to your VCF file so we can't run the code you provided. If you can't provide code that we can run, you'll need to troubleshoot on your side. I gave you some hints in my previous comment on where to start looking (incompatibility between your VCF f ...
written 16 days ago by
Hervé Pagès ♦♦ 14k
0
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... Hi Charles,
Note that this is a question about package development so should be asked on the bioc-devel mailing list.
Do you really need to support both internal representations (i.e. unstitched and stitched positions) for your CTSS objects? It sounds unlikely that you'll have long runs of adjacen ...
written 16 days ago by
Hervé Pagès ♦♦ 14k
0
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2.4k
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... Did that help? ...
written 6 weeks ago by
Hervé Pagès ♦♦ 14k
0
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101
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... Were you able to sort this out? ...
written 6 weeks ago by
Hervé Pagès ♦♦ 14k
0
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1
answer
163
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... Did that help? ...
written 6 weeks ago by
Hervé Pagès ♦♦ 14k
0
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77
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... My download failed after a few hours with some error message I don't remember.
Were you able to download the file again, uncompress it, and reproduce the error on the uncompressed file?
H. ...
written 6 weeks ago by
Hervé Pagès ♦♦ 14k
0
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Comment:
C: Warning in makeTxDbFromGFF
... Did that help? ...
written 6 weeks ago by
Hervé Pagès ♦♦ 14k
Latest awards to Hervé Pagès
Good Answer
7 months ago,
created an answer that was upvoted at least 5 times.
For A: resize (shrink/expand) GenomicRanges
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Rsamtools v 1.99.6 installation error
Popular Question
7 months ago,
created a question with more than 1,000 views.
For how to obtain base counts from BAM file at specific genomic coordinates
Popular Question
7 months ago,
created a question with more than 1,000 views.
For how to obtain base counts from BAM file at specific genomic coordinates
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
7 months ago,
created an answer that has been accepted.
For A: Rsamtools v 1.99.6 installation error
Popular Question
7 months ago,
created a question with more than 1,000 views.
For RSQLite installation question
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Calling coverage on GRanges object yields small negative values
Scholar
7 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Rsamtools v 1.99.6 installation error
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Calling coverage on GRanges object yields small negative values
Scholar
7 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Appreciated
8 months ago,
created a post with more than 5 votes.
For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
Good Answer
8 months ago,
created an answer that was upvoted at least 5 times.
For A: how to extract "Gene type" from org.Mm.eg.db?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For how to obtain base counts from BAM file at specific genomic coordinates
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Calling coverage on GRanges object yields small negative values
Scholar
11 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
Popular Question
11 months ago,
created a question with more than 1,000 views.
For unique, duplicated, order, etc... on a GRanges object
Scholar
11 months ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Popular Question
11 months ago,
created a question with more than 1,000 views.
For BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
14 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar
14 months ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
14 months ago,
created an answer that has been accepted.
For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
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