annotationConvertor: Convert between different types of gene identifiers

Description Usage Arguments Value Examples

View source: R/gsca_preprocess.R

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

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annotationConvertor(geneList, species="Hs", initialIDs="SYMBOL",
finalIDs="ENTREZID", 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 of the input. It supports all the species of OrgDb objects in AnnotationDbi. The format should be an abbreviation of the organism as setted by AnnotationDbi. For example, the commonly used ones are "Dm" ("Drosophila_melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_norvegicus"), "Mm" ("Mus_musculus"), "Ce" ("Caenorhabditis_elegans"), and etc.

initialIDs

A single character value specifying the type of initial identifiers for input geneList. The valid terms need match with the keytypes of species db such as keytypes(org.Hs.eg.db).

finalIDs

A single character value specifying the type of final identifiers for input geneList.

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 whether to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

The same data vector/matrix but with names/row names converted.

Examples

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library(org.Hs.eg.db)
## Example1: convert a named vector
x <- runif(10)
names(x) <- names(as.list(org.Hs.egSYMBOL2EG))[1:10]
xEntrez <- annotationConvertor(geneList=x, species="Hs", initialIDs="SYMBOL",
                               finalIDs="ENTREZID")

## Example2: convert a data matrix with row names as gene ids
x <- cbind(runif(10),runif(10))
rownames(x) <- names(as.list(org.Hs.egSYMBOL2EG))[1:10]
xEntrez <- annotationConvertor(geneList=x, species="Hs", initialIDs="SYMBOL",
                               finalIDs="ENTREZID")

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 11, 2018, 8:06 a.m.