Admin: Hervé Pagès
Hervé Pagès ♦♦ 12k
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Posts by Hervé Pagès
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... Hi,
A few things that might help understand what's going on:
What's "biomart ensembl hgnz_names"? I see attributes hgnc_id, hgnc_symbol, and hgnc_trans_name in the hsapiens_gene_ensembl dataset of the ENSEMBL_MART_ENSEMBL mart. Is this what you are talking about?
Where did you get your 29581 HUGO ...
written 1 day ago by
Hervé Pagès ♦♦ 12k
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... I see. It looks like the BSgenome.Hsapiens.NCBI.GRCh38.p11 destdir got created but not the inst/extdata/ folder below it.
This should be fixed in BSgenome 1.44.2. The fix should take between 24-48 hours to become available via biocLite().
Sorry for the inconvenience,
H.
...
written 1 day ago by
Hervé Pagès ♦♦ 12k
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... Hi Devin,
Just a heads up that the plan is to move away from the named RleList representation or the disjoint GRanges with metadata columns for representing genomic variables. In a not too distant future genomic variables will be better represented as metadata columns on a GPos object.
Note that t ...
written 2 days ago by
Hervé Pagès ♦♦ 12k
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Answer:
A: reads alignment statistics
... Hi,
The quickBamFlagSummary() function in Rsamtools will display various stats about the FLAG field. For example:
> quickBamFlagSummary(bamfile)
| | | mean / max
group | nb of | nb of | records
...
written 2 days ago by
Hervé Pagès ♦♦ 12k
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... Hi Lena,
Not sure what's going on. But I wonder what these RRBS_spike-in_* sequences are and where you downloaded the RRBS_spike-in_*.fa files from. The source_url field you provide points to a folder that contains the GCF_000001405.37_GRCh38.p11_genomic.fna.gz file (this is a FASTA file that conta ...
written 2 days ago by
Hervé Pagès ♦♦ 12k
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... Hi,
AFAIK SNP information for mouse can be found in different places via biomaRt:
1. In the snp_chromosome_strand attribute of the mmusculus_gene_ensembl dataset of the ENSEMBL_MART_ENSEMBL mart:
> library(biomaRt)
> mart <- useMart(host="may2012.archive.ensembl.org",
...
written 2 days ago by
Hervé Pagès ♦♦ 12k
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55
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Comment:
C: remove NA's from a DelayedArray
... I added this to DelayedArray 0.3.20:
library(DelayedArray)
A <- DelayedArray(matrix(c(NA, 1:10, NA), ncol=3))
A[is.na(A)] <- 0
A
# DelayedMatrix object of 4 x 3 doubles:
# [,1] [,2] [,3]
# [1,] 0 4 8
# [2,] 1 5 9
# [3,] 2 6 10
# [4,] 3 7 0
DelayedArra ...
written 3 days ago by
Hervé Pagès ♦♦ 12k
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55
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Comment:
C: remove NA's from a DelayedArray
... After more thoughts on this, I think we can support delayed subassignment (i.e. x[i] <- value) at least in the special case where: (1) i is a logical DelayedArray with the same dimensions as x, and (2) value is a scalar (i.e. atomic vector of length 1). That would cover x[is.na(x)] <- 0 but al ...
written 4 days ago by
Hervé Pagès ♦♦ 12k
0
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55
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... Hi,
I need to think of a more natural/intuitive way to support this but in the mean time you can use the following:
replaceNAs <- function(x, value)
{
stopifnot(is(x, "DelayedArray"),
is.vector(value),
is.atomic(value),
length(value) == 1L)
Del ...
written 4 days ago by
Hervé Pagès ♦♦ 12k
0
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... Hi Gnanendra,
Thanks for reporting this problem. Note that you should always tag your question with the package that is causing problem, which in this case is the GenomicFeatures package (where the makeTxDbFromBiomart() function belongs). The problem should now be fixed in GenomicFeatures 1.28.5.
...
written 4 days ago by
Hervé Pagès ♦♦ 12k
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