celAnnotationConvertor {HTSanalyzeR} | R Documentation

## Convert between different types of gene identifiers for Caenorhabditis Elegans

### 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")

[Package HTSanalyzeR version 2.38.0 Index]