Hoping to use Sanger's COSMIC database ("Catalogue Of Somatic Mutations In
Cancer") via biomaRt, I ran into some trouble: 'CosmicMart' connections usually
fail. A few lines to replicate the problem are included below. SessionInfo
output follows.
- Paul
library(biomaRt)
tbl <- listMarts()
dim(tbl)
colnames(tbl)
# make sure the marts are recognized, spelled properly
tbl[grep('ensembl', tbl$biomart),] # 1
tbl[grep('CosmicMart', tbl$biomart),] # 34
# this works quickly, reliably
ensembl.mart<-useMart('ensembl')
# this fails intermittently, and more often than not
cosmic.mart <- useMart('CosmicMart')
# Error in read.table(con, sep = "\t", header = FALSE, quote = "",
comment.char = "", :
# no lines available in input
# when it works, this becomes possible
tbl.datasets <- listDatasets(cosmic.mart)
grep('COSMIC', tbl.datasets$dataset, value=TRUE)
# if we get this far, this next command has not yet worked for me
useMart("CosmicMart",dataset="COSMIC61")
# Error in read.table(con, sep = "\t", header = FALSE, quote = "",
comment.char = "", :
# no lines available in input
# 'ensembl' works fine every time
ensembl.mart <-useMart('ensembl')
tbl.datasets <- listDatasets(ensembl.mart)
grep('hsapiens', tbl.datasets$dataset, value=TRUE)
human.mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
sessionInfo()
# R Under development (unstable) (2012-12-01 r61188)
# Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
#
# locale:
# [1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] biomaRt_2.15.0 BiocInstaller_1.9.5
#
# loaded via a namespace (and not attached):
# [1] compiler_2.16.0 RCurl_1.91-1 tools_2.16.0 XML_3.9-4
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