Diffficulty to use Postgwas package since Biomart web service is down
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henajose • 0
@henajose-9204
Last seen 8.5 years ago
India

Hi Bioconductor solvers,

I use Postgwas package for GWAS analysis and to perform SNP to Gene conversion use SNP2Gene function. ( I am new to R envirionment)

snps2 <- snp2gene.prox(
  snps,
  level = -1,
  biomart.config = biomartConfigs$hsapiens,
  use.buffer = FALSE,
  by.genename = TRUE,
  print.format = FALSE
)

I understand that biomaRt is not working temporarily and should use host www.ensembl.org. I tried all that was possible to reflect the change in above query, but couldnt solve it.

Any help appreciated.....

biomart Problem with biomart's listMarts function • 1.1k views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

This help site is for Bioconductor packages. As far as I can tell Postgwas used to be a CRAN package and got sent down to Crantastic because the maintainer wasn't maintaining. So not a great indication of quality or intent by the maintainer, and certainly this isn't the place to get help for that package.

That said, there are probably suitable replacements that you could consider. Not knowing exactly what you are after, I can't give much help. But if you go here and search the table (search box on the upper right) for say 'gwas', you might find something that does what you want.

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