loadGSC: Load a gene set collection

In varemo/piano: Platform for integrative analysis of omics data

Load a gene set collection

Description

Load a gene set collection, to be used in runGSA, in GMT, SBML or SIF format, or optionally from a data.frame.

Usage

loadGSC(file, type = "auto", addInfo)

Arguments

file	a character string, giving the name of the file containing the gene set collection. Optionally an object that can be coerced into a two-column data.frame, the first column containing genes and the second gene sets, representing all "gene"-to-"gene set" connections.
type	a character string giving the file type. Can be either of "gmt", "sbml", "sif". If set to "auto" the type will be taken from the file extension. If the gene-set collection is loaded into R from another source and stored in a data.frame, it can be loaded with the setting "data.frame".
addInfo	an optional data.frame with two columns, the first containging the gene set names and the second containing additional information for each gene set. Some additional info may load automatically from the different file types.

Details

This function is used to create a gene-set collection object to be used with runGSA.

The "gmt" files available from the Molecular Signatures Database (http://www.broadinstitute.org/gsea/msigdb/) can be loaded using loadGSC. This website is a valuable resource and contains several different collections of gene sets.

By using the functionality of e.g. the biomaRt package, a gene-set collection with custom gene names (matching the statistics used in runGSA) can easily be compiled into a two-column data.frame (column order: genes, gene sets) and loaded with type="data.frame".

If a sif-file is used it is assumed that the first column contains gene sets and the third column contains genes.

A genome-scale metabolic model in SBML format can be used to define gene sets. In this case, metabolites will be the gene sets, containing all the genes that code for enzymes catalyzing reactions in which the metabolite takes part in. In order to load an SBML-file it is required that libSBML and rsbml is installed. Note that the SBML loading is an experimental feature and is highly dependent on the version and format of the SBML file and requires it to contain gene associations for the reactions. By examining the returned GSC object it is easy to see if the correct gene sets were loaded.

Value

A list like object of class GSC containing two elements. The first is gsc, a list of the gene sets, each element a character vector of genes. The second element is addInfo, a data.frame containing the optional additional information.

Author(s)

Leif Varemo [e-mail] and Intawat Nookaew [e-mail]

See Also

piano, runGSA

Examples

   # Randomly generated gene sets:
   g <- sort(paste("g",floor(runif(100)*500+1),sep=""))
   g <- c(g,sort(paste("g",floor(runif(900)*1000+1),sep="")))
   g <- c(g,sort(paste("g",floor(runif(1000)*2000+1),sep="")))
   s <- paste("s",floor(rbeta(2000,0.9,1.7)*50+1),sep="")
   
   # Make data.frame:
   gsc <- cbind(g,s)
   
   # Load gene set collection from data.frame:
   gsc <- loadGSC(gsc)

varemo/piano documentation built on Sept. 19, 2022, 12:01 p.m.