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R Programming for Bioinformatics
book

R Programming for Bioinformatics

by Robert Gentleman
July 2008
Intermediate to advanced content levelIntermediate to advanced
328 pages
10h 53m
English
Chapman and Hall/CRC
Content preview from R Programming for Bioinformatics
Data Technologies 269
mart = ensMH)
> unique(rval$hgnc_symbol)
[1] "CDK2" "IL9R" "CDC2"
Exercise 8.12
What other data were returned by the call to getGene?
In order to obtain other information on the quantities of interest, the getBM
function provides a very general interface. In the code below we show how to
obtain Interpro domains for the same set of query genes as we used above.
> ensembl = useMart("ensembl",
dataset = "hsapiens_gene_ensembl")
> ipro = getBM(attributes=c("entrezgene","interpro",
"interpro_description"),
filters = "entrezgene", values = entrezID,
mart = ensembl)
> ipro
entrezgene interpro
1 1017 IPR000719
2 1017 IPR008271
3 1017 IPR001245
4
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Publisher Resources

ISBN: 9781420063677