celAnnotationConvertor: Convert between different types of gene identifiers for...

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

celAnnotationConvertor(geneList, initialIDs = "Entrez.gene", finalIDs = 
"Entrez.gene", 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", "GenBank" and "wormbase"
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", "GenBank" and "wormbase"
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 specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE)

Details

This function relies on the org.Ce.eg.db package and therefore only maps

• from any identifier to an Entrez gene id, or

• from an Entrez gene ID to any identifier

The entries that could not be mapped to any identifiers are removed from the resulting data vector/matrix.

Value

the same vector/matrix but with names/rownames corresponding to a different type of identifiers

Author(s)

Camille Terfve, Xin Wang

See Also

drosoAnnotationConvertor, mammalAnnotationConvertor, annotationConvertor

Examples

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

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