Hi, I ran into error when try to build a table of gene ID and its corresponding
name. It complained about an gene ID which could not be located from the gene
symbol table. I have used update.packages to update "GenomicFeatures" and
"org.Hs.eg.db" today. Could anybody help? Thanks.
-Kunbin
library(ShortRead)
library(GenomicFeatures)
library(org.Hs.eg.db)
map <- org.Hs.egSYMBOL
hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene")
Download the knownGene table ... annEx<-exonsBy(hg19KG, "gene") ...OK
Download the knownToLocusLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
annEx<-exonsBy(hg19KG, "gene")
GRList<-names(annEx)
geneN<-toTable(map[GRList])
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
value for "100130426" not found
Error in toTable(map[GRList]) :
error in evaluating the argument 'x' in selecting a method for function
'toTable'
sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Hs.eg.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5
[4] AnnotationDbi_1.10.2 Biobase_2.8.0 GenomicFeatures_1.0.10
[7] ShortRead_1.6.2 Rsamtools_1.0.1 lattice_0.19-11
[10] Biostrings_2.16.7 GenomicRanges_1.0.1 IRanges_1.6.8
loaded via a namespace (and not attached):
[1] biomaRt_2.4.0 BSgenome_1.17.1 grid_2.11.0 hwriter_1.3
[5] RCurl_1.4-3 rtracklayer_1.8.1 tools_2.11.0 XML_3.1-1
>
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