gene.mapping: Maps gene IDs

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/gene.mapping.R

Description

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

Usage

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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 NAs 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

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     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)

Pigengene documentation built on Nov. 8, 2020, 6:47 p.m.