Admin: Hervé Pagès
Hervé Pagès ♦♦ 13k
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Posts by Hervé Pagès
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... Hi,
In BioC 3.7, the RangesList class was replaced with the IntegerRangesList class. So:
library(GenomicRanges)
gr <- GRanges(Rle(c("A", "B"), 3), IRanges(9:4, 10))
gr
# GRanges object with 6 ranges and 0 metadata columns:
# seqnames ranges strand
# <Rle> <IRanges> ...
written 4 weeks ago by
Hervé Pagès ♦♦ 13k
0
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59
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1
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... Hi,
UCSC and Ensembl always consider the stop codon to be part of the CDS. This means that it's not considered to be part of the 3' UTR. For consistency with UCSC and Ensembl, makeTxDbFromGFF() imports the stop codon as part of the CDS. The makeTxDbFromGRanges() function, which makeTxDbFromGFF() is ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
2
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80
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... Hi all,
A new SNPlocs package is now available with the content of dbSNP build 151:
http://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP151.GRCh38
SNPlocs packages contain SNP locations and alleles for various dbSNP builds. SNPs can be looked up by chromosome, range, or rs id, using snpsBySe ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
0
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125
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Comment:
C: nearest without overlapping
... Note that the relist/unlist and split/unsplit combos are elegant, powerful, and reliable idioms, but the split/unlist combo is a risky one. It only works if the splitting factor is sorted which is indeed the case here because the class of Hits object hits is actually SortedByQueryHits.
And because ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
0
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2
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125
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Comment:
C: nearest without overlapping
... I see. Yes finding the nearest-but-not-overlapping ranges requires a little bit more work. One way to go is to take advantage of the fact that precede() and nearest() both exclude overlapping ranges:
### A version of distanceToNearest() that finds all the
### nearest-but-not-overlapping ranges in ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
0
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1
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65
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... Hi,
In other words you want to skip matches that overlap with a previous match. Note that this is what regular expressions do:
> gregexpr("TAT", "ATATATATGCAT")
[[1]]
[1] 2 6
attr(,"match.length")
[1] 3 3
attr(,"index.type")
[1] "chars"
attr(,"useBytes")
[1] TRUE
But in your case it seems th ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
0
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2
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125
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Answer:
A: nearest without overlapping
... Hi,
Don't remove anything from subject **before** you call distanceToNearest() or you will loose hits that you want to keep:
library(GenomicRanges)
x <- GRanges(c("chr1:2-4", "chr1:5-8"))
subject <- GRanges("chr1:7-10")
distanceToNearest(x, subject)
# Hits object with 2 hits and 1 metadata ...
written 6 weeks ago by
Hervé Pagès ♦♦ 13k
0
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1
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144
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1
answers
... 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 10 weeks ago by
Hervé Pagès ♦♦ 13k
0
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1
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104
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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 10 weeks ago by
Hervé Pagès ♦♦ 13k
0
votes
1
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92
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1
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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 10 weeks ago by
Hervé Pagès ♦♦ 13k
Latest awards to Hervé Pagès
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: Extracting Coordinates of startcodon from Grangeslist
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Scholar
3 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Extracting Coordinates of startcodon from Grangeslist
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
Commentator
13 months ago,
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For C: Error in GRanges: could not find symbol "recursive" in environment of the generi
Scholar
13 months ago,
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For A: Extracting Coordinates of startcodon from Grangeslist
Scholar
13 months ago,
created an answer that has been accepted.
For A: coverage() output SimpleRleList cannot be converted to GRanges
Teacher
13 months ago,
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For A: overlapsAny for elements in GRangesList
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: How do I merge a list of GRanges?
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: about setdiff() and meta-information in GRanges
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: extract subsequence(s) from DNAStringSet with getSeq
Popular Question
13 months ago,
created a question with more than 1,000 views.
For unique, duplicated, order, etc... on a GRanges object
Scholar
13 months ago,
created an answer that has been accepted.
For A: makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
Scholar
13 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
13 months ago,
created an answer that has been accepted.
For A: A bug of "seqlevels<-" on TxDb
Scholar
13 months ago,
created an answer that has been accepted.
For A: about setdiff() and meta-information in GRanges
Scholar
13 months ago,
created an answer that has been accepted.
For A: extract subsequence(s) from DNAStringSet with getSeq
Scholar
13 months ago,
created an answer that has been accepted.
For A: Feature request: syntax for dropping unused seqlevels in GRanges objects
Scholar
13 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
Teacher
13 months ago,
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For A: Error when running "locateVariants" function in "VariantAnnotation" package
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13 months ago,
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For A: subsetByOverlaps with Multimapping
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13 months ago,
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For A: How do I merge a list of GRanges?
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