ids2indices: Convert Gene Identifiers to Indices for Gene Sets
In hdeberg/limma: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

Make a list of gene identifiers into a list of indices for gene sets.

1	ids2indices(gene.sets, identifiers, remove.empty=TRUE)

`gene.sets`	list of character vectors, each vector containing the gene identifiers for a set of genes.
`identifiers`	character vector of gene identifiers.
`remove.empty`	logical, should sets of size zero be removed from the output?

This function used to create input for romer, mroast and camera function. Typically, identifiers is the vector of Entrez Gene IDs, and gene.sets is obtained constructed from a database of gene sets, for example a representation of the Molecular Signatures Database (MSigDB) downloaded from http://bioinf.wehi.edu.au/software/MSigDB.

list of integer vectors, each vector containing the indices of a gene set in the vector identifiers.

Gordon Smyth and Yifang Hu

romer, mroast, camera

There is a topic page on 10.GeneSetTests.

## Not run: 

download.file("http://bioinf.wehi.edu.au/software/MSigDB/human_c2_v5p2.rdata", 
	      "human_c2_v5p2.rdata", mode = "wb")

load("human_c2_v5p2.rdata")
c2.indices <- ids2indices(Hs.c2, y$genes$GeneID)
camera(y, c2.indices, design)


## End(Not run)