[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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber



More information about the Bioconductor mailing list