Admin: Hervé Pagès
Hervé Pagès ♦♦ 13k
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- Joined:
- 12 years, 6 months ago
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Posts by Hervé Pagès
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... That seems to have addressed the issue. I consequently bumped the version of all packages that have Rhtslib in their LinkingTo field (e.g. csaw, bamsignals, deepSNV, etc...), but only in release (RELEASE_3_7 branch) for now. See for example commit 6ea86c79cfbc2b9d765ed31b35364b5eb39c7671 in the RELE ...
written 13 days ago by
Hervé Pagès ♦♦ 13k
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... Hi Dario,
Here is a fast solution based on an unexported utility defined in the S4Vectors package:
connectedCompEdges <- function(concomp)
{
hits <- S4Vectors:::makeAllGroupInnerHits(lengths(concomp), hit.type=1L)
nodes <- unlist(concomp, use.names=FALSE)
from <- nodes[que ...
written 17 days ago by
Hervé Pagès ♦♦ 13k
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... Hi James,
Those changes are documented as changes to GRanges objects and their derivatives (GPos is a subclass of GRanges). The change in question is this:
GenomicRanges now is a List subclass. This means that GRanges objects and their derivatives are now considered list-like objects (even thoug ...
written 17 days ago by
Hervé Pagès ♦♦ 13k
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... Hi Stephanie,
The recommended replacement is to loop over seq_along(x) instead of x so:
lapply(seq_along(x), function(i) print(x[i]))
Cheers,
H.
...
written 17 days ago by
Hervé Pagès ♦♦ 13k
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... Hi Aaron,
We have /usr/local/opt/xz/lib/liblzma.5.dylib on our Mac builders merida1 and merida2. It got installed as a dependency when we used brew to install some other component, maybe when we did brew install openssl or brew install python3 or brew install libxml2, hard to tell. For some reason, ...
written 19 days ago by
Hervé Pagès ♦♦ 13k
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... Thanks for the report. This should be fixed in GenomicRanges 1.32.3 (BioC 3.7) and 1.33.3 (BioC devel). Both versions of GenomicRanges should become available via biocLite() in the next 48 hours.
Cheers,
H.
...
written 4 weeks ago by
Hervé Pagès ♦♦ 13k
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... No plans to support this in the immediate future. I'm putting this on the TODO list and will get to it after the BioC 3.7 release (scheduled for May 1st). In the mean time, you can work around this by coercing to GRanges first. I recognize that this defeats the purpose of using a GPos object in the ...
written 10 weeks ago by
Hervé Pagès ♦♦ 13k
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... It's a DNAStringSetList object, not a DNAStringSet object. A DNAStringSetList object is a list-like object where each list element is a DNAStringSet object. Like with an ordinary list, you can extract individual list elements of a DNAStringSetList object with [[ or unlist the object with unlist(). B ...
written 3 months ago by
Hervé Pagès ♦♦ 13k
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... Hi,
Let's separate the 2 issues you seem to be having: (1) the use of different chromosome naming conventions for Athaliana between plantsmart28 and UCSC, and (2) getPromoterSeq() failing to extract out-of-bounds ranges.
Issue (1) can be addressed by setting the same sequence style on the 2 object ...
written 3 months ago by
Hervé Pagès ♦♦ 13k
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... Please ask this as a new question. Thanks!
...
written 3 months ago by
Hervé Pagès ♦♦ 13k
Latest awards to Hervé Pagès
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4 weeks ago,
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For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
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11 months ago,
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For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
Popular Question
11 months ago,
created a question with more than 1,000 views.
For unique, duplicated, order, etc... on a GRanges object
Teacher
11 months ago,
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For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
Teacher
11 months ago,
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For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
11 months ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Scholar
11 months ago,
created an answer that has been accepted.
For A: subsetByOverlaps with Multimapping
Scholar
11 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar
11 months ago,
created an answer that has been accepted.
For A: Extracting Coordinates of startcodon from Grangeslist
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: overlapsAny for elements in GRangesList
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11 months ago,
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For A: How do I merge a list of GRanges?
Teacher
11 months ago,
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For A: about setdiff() and meta-information in GRanges
Teacher
11 months ago,
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For A: extract subsequence(s) from DNAStringSet with getSeq
Scholar
11 months ago,
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For A: How do I merge a list of GRanges?
Scholar
11 months ago,
created an answer that has been accepted.
For A: Generic functions for DataFrames of Rle objects ?
Scholar
11 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
11 months ago,
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For A: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
Scholar
11 months ago,
created an answer that has been accepted.
For A: about setdiff() and meta-information in GRanges
Scholar
11 months ago,
created an answer that has been accepted.
For A: extract subsequence(s) from DNAStringSet with getSeq
Scholar
11 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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11 months ago,
created an answer that has been accepted.
For A: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
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11 months ago,
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For A: Error when running "locateVariants" function in "VariantAnnotation" package
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11 months ago,
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For Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
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11 months ago,
created a question with more than 1,000 views.
For overlap regions between two GRanges (or GRangesList)
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