Description Usage Arguments Value Examples
View source: R/annotateFromBiomart.R
Annotate your Expression Set with biomaRt
1 2 3 4 | annotateFromBiomart(obj, genes = featureNames(obj),
filters = "ensembl_gene_id", attributes = c("ensembl_gene_id",
"hgnc_symbol", "chromosome_name", "start_position", "end_position"),
biomart = "ensembl", dataset = "hsapiens_gene_ensembl", ...)
|
obj |
ExpressionSet object. |
genes |
Genes or rownames of the ExpressionSet. |
filters |
getBM filter value, see getBM help file. |
attributes |
getBM attributes value, see getBM help file. |
biomart |
BioMart database name you want to connect to. Possible database names can be retrieved with teh function listMarts. |
dataset |
Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart). |
... |
Values for useMart, see useMart help file. |
ExpressionSet object with a fuller featureData.
1 2 3 4 5 6 7 8 | data(skin)
# subsetting and changing column name just for a silly example
skin <- skin[1:10,]
colnames(fData(skin)) = paste("names",1:6)
biomart<-"ENSEMBL_MART_ENSEMBL";
genes <- sapply(strsplit(rownames(skin),split="\\."),function(i)i[1])
newskin <-annotateFromBiomart(skin,genes=genes,biomar=biomart)
head(fData(newskin)[,7:11])
|
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