idMap {EnrichmentBrowser} | R Documentation |
Functionality to map the rownames of a SummarizedExperiment between common gene ID types such as ENSEMBL and ENTREZ.
idMap(se, org = NA, from = "ENSEMBL", to = "ENTREZID") idTypes(org)
se |
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 names of argument 'se'. Defaults to 'ENSEMBL'. |
to |
Gene ID type to which should be mapped. Corresponds to the gene ID type the featuresNames of argument 'se' should be updated with. Defaults to 'ENTREZID'. |
The function 'idTypes' 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.
idTypes: character vector listing the available gene ID types for the mapping;
idMap: 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 se <- makeExampleData("SE", nfeat=3, nsmpl=3) names(se) <- paste0("ENSG00000000", c("003","005", "419")) se <- idMap(se, org="hsa")