Convert Gene Identifiers to Indices for Gene Sets
Make a list of gene identifiers into a list of indices for gene sets.
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
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.