[Bioc-devel] proposal for additional seqlevelsStyle

Robert Castelo robert@c@@te|o @end|ng |rom up|@edu
Tue Dec 10 23:19:28 CET 2019

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 think that 'seqlevelsStyle()' from the GenomeInfoDb package is one of 
the most influential contributions to human genetics, if you think about 
the time invested by researchers in parsing and changing between 
different styles of chromosome names :)


On 06/12/2019 15:03, Vincent Carey wrote:
> 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
> 1    FALSE TRUE FALSE    1 chr1   ch1       1
> 2    FALSE TRUE FALSE    2 chr2   ch2       2
> that includes the values for "NCBI reference sequence names"
> See https://www.ncbi.nlm.nih.gov/nuccore/568815581 for one report on chr17,
> and
> https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39
> for a table that includes the Genbank labels.
> Should I just file a PR at https://github.com/Bioconductor/GenomeInfoDb/ after
> testing?

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