mammalAnnotationConvertor: Convert between different types of identifiers for mammalian...

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

Description

This function converts an initial data vector named by non-entrez ids to the same vector but with entrez ids, and vice versa. Genes for which no mapping were found will be removed. This function can also take a matrix, with gene identifiers as row names.

Usage

mammalAnnotationConvertor(geneList, initialIDs = "Entrez.gene", finalIDs = 
"Entrez.gene", species = "Hs", keepMultipleMappings = TRUE, verbose=TRUE)

Arguments

geneList	a named integer or numeric vector, or a matrix with rows named by gene identifiers
initialIDs	a single character value specifying the type of initial identifiers for input 'geneList'. The current version can take one of the following types: "Ensembl.transcript", "Ensembl.prot", "Ensembl.gene", "Entrez.gene", "RefSeq", "Symbol" and "GenBank".
finalIDs	a single character value specifying the type of final identifiers to which users want to convert. The current version can take one of the following types: "Ensembl.transcript", "Ensembl.prot", "Ensembl.gene", "Entrez.gene", "RefSeq", "Symbol" and "GenBank"
species	a single character value specifying the species: "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus") or "Mm" ("Mus_musculus")
keepMultipleMappings	a single logical value. If TRUE, the function keeps the entries with multiple mappings (first mapping is kept). If FALSE, the entries with multiple mappings will be discarded.
verbose	a single logical value indicating to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE)

Details

This function removes the genes for which no mapping was found. This function relies on the org.Hs.eg.db/org.Mm.eg.db/org.Rn.eg.db packages and therefore only maps from any identifier to an Entrez gene ID or from an Entrez gene ID to any identifier.

Value

the same data vector/matrix but with another type of identifiers as names/row names

Author(s)

Camille Terfve, Xin Wang

See Also

drosoAnnotationConvertor, celAnnotationConvertor, annotationConvertor

Examples

##example 1: convert a named vector
library(org.Hs.eg.db)
x <- runif(10)
names(x) <- names(as.list(org.Hs.egSYMBOL2EG))[1:10]
xEntrez <- mammalAnnotationConvertor(geneList=x, initialIDs="Symbol",
finalIDs="Entrez.gene", species="Hs")
##example 2: convert a data matrix with row names as gene ids
library(org.Hs.eg.db)
x <- cbind(runif(10), runif(10))
rownames(x) <- names(as.list(org.Hs.egSYMBOL2EG))[1:10]
xEntrez <- mammalAnnotationConvertor(geneList=x, initialIDs="Symbol",
finalIDs="Entrez.gene", species="Hs")

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.