annotationConvertor: Convert between different types of gene identifiers

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

annotationConvertor(geneList, species="Dm", 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
species	a single character value specifying the species for which the data should be read. The current version supports one of the following species: "Dm" ("Drosophila_melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), "Mm" ("Mus_musculus") and "Ce" ("Caenorhabditis_elegans").
initialIDs	a single character value specifying the type of initial identifiers for input 'geneList'. Current version can take one of the following types: "Ensembl.transcript", "Ensembl.prot", "Ensembl.gene", "Entrez.gene", "RefSeq", "Symbol" and "GenBank" for all supported species; "Flybase", "FlybaseCG" and "FlybaseProt" in addition for Drosophila Melanogaster; "wormbase" in addition for Caenorhabditis Elegans.
finalIDs	a single character value specifying the type of initial identifiers for input 'geneList'. Current version can take one of the following types: "Ensembl.transcript", "Ensembl.prot", "Ensembl.gene", "Entrez.gene", "RefSeq", "Symbol" and "GenBank" for all supported species; "Flybase", "FlybaseCG" and "FlybaseProt" in addition for Drosophila Melanogaster; "wormbase" in addition for Caenorhabditis Elegans.
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

The entries that could not be mapped to any identifiers are removed from the resulting data vector/matrix. This function relies on the org.Dm.eg.dbpackage 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 names/row names converted.

Author(s)

Xin Wang, Camille Terfve

See Also

mammalAnnotationConvertor, celAnnotationConvertor, drosoAnnotationConvertor

Examples

library(org.Dm.eg.db)
##example 1: convert a named vector
x<-runif(10)
names(x)<-names(as.list(org.Dm.egSYMBOL2EG))[1:10]
xEntrez<-annotationConvertor(geneList=x, species="Dm", 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.Dm.egSYMBOL2EG))[1:10]
xEntrez<-annotationConvertor(geneList=x, species="Dm", initialIDs="Symbol", 
finalIDs="Entrez.gene")

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