convertSmc: Convert Entrez ID based "smc" object

In PGSEA: Parametric Gene Set Enrichment Analysis

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 <[e-mail]>

Examples

## Not run: 
	download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")
	
	datadir <- system.file("extdata", package = "PGSEA")
	sample <- readGmt(file.path(datadir, "sample.gmt"))
	
	converted <- convertSmc(sample[1:2],"h","r")
	str(converted)

## End(Not run)

PGSEA documentation built on April 28, 2020, 8:28 p.m.