map.ids {EnrichmentBrowser} | R Documentation |
Functionality to map feature names of an expression set between common gene ID types such as ENSEMBL and ENTREZ.
id.types( org ) map.ids( eset, org=NA, from="ENSEMBL", to="ENTREZID" )
eset |
An object of class |
org |
Organism in KEGG three letter code, e.g. ‘hsa’ for ‘Homo sapiens’. See references. |
from |
Gene ID type from which should be mapped. Corresponds to the gene ID type of the featureNames of argument 'eset'. Defaults to 'ENSEMBL'. |
to |
Gene ID type to which should be mapped. Corresponds to the gene ID type the featuresNames of argument 'eset' should be updated with. Defaults to 'ENTREZID'. |
The function 'id.types' lists the valid values which the arguments 'from' and 'to' can take. This corresponds to the names of the available gene ID types for the mapping.
id.types: character vector listing the available gene ID types for the mapping;
map.ids: An object of SummarizedExperiment
.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
KEGG Organism code http://www.genome.jp/kegg/catalog/org_list.html
SummarizedExperiment
,
mapIds
, keytypes
# create an expression dataset with 3 genes and 3 samples eset <- make.example.data("eset", nfeat=3, nsmpl=3) names(eset) <- paste0("ENSG00000000", c("003","005", "419")) eset <- map.ids(eset, org="hsa")