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
https://simplystatistics.org/2013/01/31/paste0-is-statistical-computings-most-influential-contribution-of-the-21st-century
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 :)
robert.
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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