convertSmc {PGSEA} | R Documentation

## Convert Entrez ID based "smc" object

### Description

This function will convert the Entrez IDs of an smc object to the corresponding Entrez IDs from a different species. Data from the homologene project is downloaded and used within this function.

### Usage

    convertSmc(mcs, fromSpecies = "h", toSpecies = "r",hgX="./homologene.data")

### Arguments

`mcs` | a list of "smc" objects
`fromSpecies` | character - a single letter describing the species to convert from ie, h=human, r= rat, etc..
`toSpecies` | character - a single letter describing the species to convert to ie, h=human, r= rat, etc..
`hgX` | character - file name of homologene data file

### Details

This function will not work if you have not downloaded the homologene data file. Please use this command to do so: download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")

### Value

a list of converted "smc" objects

### Author(s)

Karl Dykema <karl.dykema@vai.org>

### Examples

    ## Not run:
            download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")

            datadir <- system.file("data", package = "PGSEA")
            sample <- readGmt(file.path(datadir, "sample.gmt"))

            converted <- convertSmc(sample[1:2],"h","r")
            str(converted)
    ## End(Not run)

[Package PGSEA version 1.6.0 Index]