| org.Hs.egALIAS2EG {org.Hs.eg.db} | R Documentation |
org.Hs.egALIAS is an R object that provides mappings between common gene symbol identifiers and entrez gene identifiers.
Each gene symbol maps to a named vector containing the corresponding entrez gene identifier. The name of the vector corresponds to the gene symbol. Since gene symbols are sometimes redundantly assigned in the literature, users are cautioned that this map may produce multiple matching results for a single gene symbol. Users should map back from the entrez gene IDs produced to determine which result is the one they want when this happens.
Because of this problem with redundant assigment of gene symbols, is it never advisable to use gene symbols as primary identifiers.
This mapping includes ALL gene symbols including those which are already listed in the SYMBOL map. The SYMBOL map is meant to only list official gene symbols, while the ALIAS maps are meant to store all used symbols.
Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA With a date stamp from the source of: 2017-Nov6
https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
AnnotationDb-class for use of
the select() interface.
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.
## Bimap interface:
# Convert the object to a list
xx <- as.list(org.Hs.egALIAS2EG)
# Remove pathway identifiers that do not map to any entrez gene id
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
# The entrez gene identifiers for the first two elements of XX
xx[1:2]
# Get the first one
xx[[1]]
}