ids2indices {limma} | R Documentation

## Convert Gene Identifiers to Indices for Gene Sets

### Description

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

### Usage

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

### Arguments

`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?

### Details

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.

### Value

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

### Author(s)

Gordon Smyth and Yifang Hu

### See Also

`romer`, `mroast`, `camera`

There is a topic page on 10.GeneSetTests.

### Examples

    ## 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)

[Package limma version 3.38.3 Index]