Thanks Hervé,
this looks very useful!!!
robert.
On 03/07/2020 07:49, Hervé Pagès wrote:
Hi Vince, Robert, Kasper,
I've done some work on this. Starting with GenomeInfoDb_1.25.7 the
seqlevelsStyle() setter has 2 major improvements:
1. It knows how to rename contigs and scaffolds, not just
This looks great Hervé!
I will work on incorporating this into tximeta when RefSeq
transcriptomes are used.
I second Robert's position that seqlevelsStyle() is one of the most
influential contributions to human genetics.
___
Bioc-devel@r-project.org
Hi Vince, Robert, Kasper,
I've done some work on this. Starting with GenomeInfoDb_1.25.7 the
seqlevelsStyle() setter has 2 major improvements:
1. It knows how to rename contigs and scaffolds, not just the chromosomes:
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
seqinfo(txdb)
# Seqinfo
If the chromosome name depends on the assembly, that makes GenomeInfoDb
even more useful and necessary. Provided it is supported of course.
On Fri, Dec 13, 2019 at 11:45 AM Vincent Carey
wrote:
> I tried an inline png but I think it was rejected by bioc-devel. Here's
> another try.
>
> On
I tried an inline png but I think it was rejected by bioc-devel. Here's
another try.
On Fri, Dec 13, 2019 at 11:40 AM Vincent Carey
wrote:
> Thanks -- It is good to know more about the complications of adding
> seqlevelsStyle elements.
> I am not sure how pervasive this will be in SNP
hi Hervé,
i didn't know about this new sequence style until Vince posted his
message and we briefly talked about it at the European BioC meeting this
week in Brussels. however, i didn't know that the style was specific to
a particular assembly. i have no use case of this at the mome moment,
Hi Vince, Robert,
Looks like Vince wants the RefSeq accession e.g. NC_17.11 for chrom
17 in the GRCh38.
@Robert: Is this what you're also interested in?
The problem is that the RefSeq accessions are specific to a particular
assembly (e.g. NC_17.11 for chrom 17 in GRCh38 but
I second this, and would suggest to name the style as 'GRC' for "Genome
Reference Consortium".
thanks Vince for bringing this up, being able to easily switch between
genome styles is great.
if 'paste0()' in R is one of the most influential contributions to
statistical computing
I raised this issue previously with little response.
I'd propose that we add a column or two to genomeStyles()$Homo_sapiens
> head(genomeStyles()$Homo_sapiens, 2)
circular auto sex NCBI UCSC dbSNP Ensembl
1FALSE TRUE FALSE1 chr1 ch1 1
2FALSE TRUE FALSE2 chr2 ch2
