Package HomoVert. November 10, 2010

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1 Package HomoVert November 10, 2010 Version Date Title HomoVert: Functions to convert Gene IDs between species Author Matthew Fero Maintainer Matthew Fero Depends R (>= 2.4.0) Suggests HomoVert is a package that contains a Homologene conversion table (Build 64) and functions that use this table to convert Entrez Gene IDs from one species to another. License GPL version 2 or newer URL R topics documented: get.homo homo.frame homo.vect HomoVert Index 6 get.homo Download a current Homologene conversion table This function will download conversion tables from the Homologene FTP site. get.homo(ftp.url, destdir, build) 1

2 2 homo.frame Arguments ftp.url destdir build The url of the ftp site (defaults is "ftp://ftp.ncbi.nih.gov/pub/homologene". The (optional) directory to which homologene.data should be downloaded. Homologene build number. Default is the current build. Ignored if ftp.url is given. Details The location of the downloaded file is given by tempdir(), unless a destdir argument was specified. The table will be imported into R has homologene.data overwriting any other prior object by that name. To use homologene.data for gene ID conversions use it as the homo argument in the homo.vect or homo.frame functions. Returns a homologene.data as a global data.frame (overwrites any prior object called homologene.data. See homo.vect and homo.frame to use homologene tables to convert IDs from one species to another. Examples library(homovert) # Load the 'HomoVert' package get.homo() # Download and import the current 'homologene.data' into R. homo.frame Function to convert Entrez Gene IDs between species This function will add Entrez GeneID and Symbols from another species onto a dataframe. homo.frame(data, Gene.col=1, Spec1="human", Spec2="mouse", type="common", Tax, homo) Arguments data Gene.col Spec1 Spec2 type Tax homo A dataframe containing a column of Entrez Gene IDs The name or number of the column with Gene IDs The name of the species to be converted from The name of the species to be converted to The type of species name (either "common", "latin", or "tax\_id") Optional taxonomy list (for species not listed in TaxID) The Homologene conversion list.

3 homo.vect 3 Returns the original data frame with additional columns: x.geneid, and x.symbol (where x is the abbreviation of Spec2). The orginal GeneIDs are listed in column 1 and are renamed y.geneid where y is the Spec1 abbreviation. HomoVert the dataset which includes the Homologene conversion table, and homo.vect a function that converts a GeneID list. Examples library(homovert) # Load the 'HomoVert' package data(homovert, package="homovert") # Load default Taxonomy IDs and Homologene data test = data.frame(geneid= c(1,2), Details= c("test gene 1", "test gene 2")) # View the test matrix... test # Convert human IDs to mouseids and append this onto the test matrix homo.frame(test, Gene.col=1) homo.vect Function to convert Entrez Gene IDs between species This function will convert Entrez Gene IDs from one species to another. It returns results as a data frame with the converted IDs listed in the GeneID column. Other columns include the corresponding Homologene ID, the gene symbol, the taxonomy id of which ever specie is chosen plus the protein IDs and protein accession numbers. homo.vect(input, Spec1="human", Spec2="mouse", type="common", Tax, homo) Arguments input Spec1 Spec2 type Tax homo A vector of Entrez Gene IDs. The name of the species to be converted from The name of the species to be converted to The type of species name (either common, latin, or tax_id) Optional taxonomy list (for species not listed in TaxID) Optional homologene conversion table. Default uses built-in table Returns a data frame listing with columns: HID, tax\_id, GeneID, Symbol, Prot.gi, and Prot.acc.

4 4 HomoVert HomoVert the dataset which includes the Homologene conversion table, and homo.frame an alterate function which annoates converted GeneIDs onto a dataframe. The current homologene data can be downloaded with get.homo Examples library(homovert) # Load the 'HomoVert' package data(homovert, package="homovert") # Load default Taxonomy IDs and Homologene data TaxID # List taxonomy IDs of some common animals. Hs.example # A small set of human Gene IDs # Convert the human Gene IDs to mouse Gene IDs Mm.homo <- homo.vect(input = Hs.example) ## Import the most recent Homologene data: # (First download 'Homologene.data' from the FTP site, listed above, # and place it in the working direcory). # Homo.new <- read.delim2(file = "Homologene.data", header = FALSE, as.is=true) # colnames(homo.new) <- colnames(homo) # Save the output to a tab-delimited text file: # write.table(mm.homo, file = "Mm.homo.txt", row.names = FALSE, sep="\t") # Save a list of all human homologene IDs: # write.table(homo[homo$tax_id == 9606,], file = "Hh.homo.data.xls", # row.names = FALSE, sep="\t") HomoVert Homologene conversion table and Taxonomy IDs Details A dataset provided with the HomoVert package which includes a Homologene conversion table, a Taxonomy list, and sample data. data(homovert) # load the Homologene data set (build 64) The built-in Homologene conversion table will be loaded and returned as a dataframe called Homo. Also returned are TaxID (a table of Taxonomy IDs) and Hs.example a vector of 5 H.sapiens Gene IDs. TaxID A listing of the common names, latin names, and taxonomy IDs. Hs.example A vector of 8 human GeneIDs. Homo A data frame with the following columns: HID homologene IDs

5 HomoVert 5 tax_id GeneID Symbol Prot.gi Prot.acc taxonomy IDs, e.g = human Entrez Gene IDs Gene symbols protein IDs protein accession numbers Source Matthew Fero, Fred Hutchinson Cancer Research Center, Seattle WA. See homo.vect converts a vector of Gene IDs from one species to another using homologene conversion table. See homo.frame to annotate GeneIDs from a different species onto a dataframe.

6 Index Topic datasets HomoVert, 4 Topic methods get.homo, 1 homo.frame, 2 homo.vect, 3 get.homo, 1, 3 Homo (HomoVert), 4 homo.frame, 2, 2, 3, 5 homo.vect, 2, 3, 3, 5 HomoVert, 3, 4 Hs.example (HomoVert), 4 TaxID (HomoVert), 4 6