convertFunctionalCategories: Function to convert Entrez gene ID-based functional...

In uc-bd2k/CLEAN: Clustering Enrichment Analysis

Function to convert Entrez gene ID-based functional categories from one species to another using the Homologene database

Description

This function loads the Homologene table and a list of functional categories and converts Entrez gene IDs from one species to another. Currently implemented species are "h" (Homo sapiens), "m" (Mus musculus), and "r" (Rattus norvegicus).

Use the following command to download the Homologene table into the working directory: > download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")

This function was adapted from from convertSmc() of the PGSEA package.

Usage

convertFunctionalCategories(functionalCategories, fromSpecies = "h", toSpecies = "r", homologTable = "./homologene.data")
convertGeneTable(geneTable, fromSpecies = "h", toSpecies = "r", homologTable = "./homologene.data")

Arguments

functionalCategories	A list of functional categories.
geneTable	A matrix or data.frame where the first column contains gene IDs and the second column contains p-values.
fromSpecies	Species the functional categories are currently defined for. Currently implemented species are "h" (Homo sapiens), "m" (Mus musculus), and "r" (Rattus norvegicus).
toSpecies	Species the functional categories are to be converted to. Currently implemented species are "h" (Homo sapiens), "m" (Mus musculus), and "r" (Rattus norvegicus).
homologTable	File name of the Homologene Table.

Author(s)

Johannes Freudenberg

See Also

runCLEAN, GRS

Examples

## not run
# download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")
# library(CLEAN.Hs)
# data(geneRIFs.Hs)
# geneRIFs.Rn <- geneRIFs.Hs
# geneRIFs.Rn$RIFterm2Genes <- convertFunctionalCategories(geneRIFs.Hs$RIFterm2Genes)
#
# data(bCa)
# geneTable <- convertGeneTable(bCa$Schmidt.pValues)

uc-bd2k/CLEAN documentation built on Oct. 19, 2024, 11:45 p.m.