convertSmc {PGSEA} | R Documentation |
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.
convertSmc(mcs, fromSpecies = "h", toSpecies = "r",hgX="./homologene.data")
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 |
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")
a list of converted "smc" objects
Karl Dykema <karl.dykema@vai.org>
## 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)