[BioC] Map the enriched chromosome bands to entrez genes
Wolfgang Huber
whuber at embl.de
Wed Sep 8 10:41:59 CEST 2010
Dear Xi,
try this:
library("org.Hs.egCHR")
uu = as.list( revmap(org.Hs.egMAP) )
print(uu)
i = grep("^1q", names(uu))
uu[i]
length(unique(unlist(uu[i])))
# [1] 1796
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-09-07 r52876)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=la_AU.utf8 LC_NUMERIC=C
[3] LC_TIME=la_AU.utf8 LC_COLLATE=la_AU.utf8
[5] LC_MONETARY=C LC_MESSAGES=la_AU.utf8
[7] LC_PAPER=la_AU.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=la_AU.utf8 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_1.11.4 Biobase_2.9.0 fortunes_1.3-7
loaded via a namespace (and not attached):
[1] tools_2.12.0
Xi Zhao scripsit 08/09/10 10:10:
>
> Dear list,
>
> Im struggling retrieving the full list of the entrez geneIDs for each of the enriched chromosome bands (obtained by "GOstats").
>
> revmap(org.Hs.egCHR) doesnt give the entrezIDs for the sub-arms, only for the whole arm:
>
> mget(c("16", "1q"), revmap(org.Hs.egCHR), ifnotfound=NA) # Map between Entrez Gene IDs and Chromosomes
> $`1q`
> [1] NA
>
> revmap(org.Hs.egMAP) only gives a few genes locate on that chromosome... (or did I do it wrong?)
>
> mget(c("16", "1q"), revmap(org.Hs.egMAP), ifnotfound=NA) # Map between Entrez Gene Identifiers and cytogenetic maps/bands
> $`16`
> [1] "8720"
> $`1q`
> [1] "4030" "7254" "100113374" "100302291" "100313962"
>
> Any suggestion / hint is appreciated!
>
> Kindest regards,
> Xi
>
>
>
>
> [[alternative HTML version deleted]]
>
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--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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