gene.mapping {Pigengene} | R Documentation

## Maps gene IDs

### Description

Takse as input gene IDs in a convention, say REFSEQ, and converts them to another convention.

### Usage

    gene.mapping(ids, inputType = "REFSEQ", outputType = "SYMBOL",
      leaveNA = TRUE, inputDb = "Human", outputDb = inputDb,
      verbose = 0)

### Arguments

`ids` | A character vector of input gene IDs
`inputType` | The type of input IDs.
`outputType` | The type of output IDs. If it is a character vector, mapping will be done for each element.
`leaveNA` | If `TRUE`,the IDs that were not matched are left with `NA`s in the second column of the output, otherwise the input IDs are returned.
`inputDb` | The input data base. Use `org.Hs.eg.db` for human and `org.Mm.eg.db` for mouse. The default "Human" character uses the former.
`outputDb` | The output data base. If it is a list, mapping will be done for each element.
`verbose` | The integer level of verbosity. 0 means silent and higher values produce more details of computation.

### Details

It can map homologous genes between species e.g. from mouse to human. If more than 1 ID found for an input gene, only one of them is returned.

### Value

A matrix of characters with 3 columns: input, output1, and output2. The last one is guaranteed not to be `NA`.

### Author(s)

Amir Foroushani, Habil Zare, and Rupesh Agrahari

### References

Pages H, Carlson M, Falcon S and Li N. AnnotationDbi: Annotation Database Interface. R package version 1.32.3.

### See Also

`AnnotationDb-class`, `org.Hs.eg.db` `org.Mm.eg.db`

### Examples

         library(org.Hs.eg.db)
         g1 <- gene.mapping(ids="NM_001159995")
         print(g1)

         ## Mapping to multiple convention
         library(org.Mm.eg.db)
         g2 <- gene.mapping(ids=c("NM_170730", "NM_001013580"),
            inputType="REFSEQ", inputDb=org.Mm.eg.db,
            outputType=c("SYMBOL","ENTREZID"),
            outputDb=list(org.Hs.eg.db,org.Mm.eg.db), verbose=1)
         print(g2)

[Package Pigengene version 1.12.0 Index]