This mapping has been deprecated and will no longer be available after bioconductor 2.6. See the details section for how you can live without it. For now, it is a map of UCSC "Known Gene" accession numbers with Entrez Gene identifiers

Description

org.Hs.egUCSCKG is an R object that contains mappings between Entrez Gene identifiers and UCSC "Known Gene" accession numbers.

Details

This object is a simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene to UCSC "Known Gene" Accession Numbers. Please be advised that UCSC "Known Genes" are not more like putative transcripts transcript identifiers than they are gene identifiers.

Mappings were based on data provided by: UCSC Genome Bioinformatics (Homo sapiens)

With a date stamp from the source of: 2017-Oct9

This mapping is based on the very latest build available at UCSC for this organism as of March 2010. 2.6 is the last release where you can expect it to be here. The GenomicFeatures package contains functionality that replaces the need for this mapping. Please see the GenomicFeatures vignette for details on how to use it.

See Also

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
x <- org.Hs.egUCSCKG
# Get the entrez gene IDs that are mapped to a UCSC KG ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the UCSC gene IDs for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}