gs2edge: Create Gene set matrices

In wiscstatman/Rolemodel: Gene-set analysis via MFA

Description

Given a vector of genes and a gene set library, create input objects for enrichment functions

Usage

gs2edge(idlist, idtype = c("SYMBOL", "ENTREZID", "REFSEQ", "ENSEMBL", "ACCNUM", "UNIPROT", "PMID"), lib, library.loc = NULL, n.upp = 50, n.low = 5, sets = c("GO", "KEGG"))

Arguments

idlist	character vector of gene ids for which to test enrichment of gene set categories
idtype	character, type of gene ids: SYMBOL, ENTREZID, REFSEQ, ENSEMBL, ACCNUM, UNIPROT, PMID. Default is SYMBOL
lib	character, organism library, e.g. "org.Hs.eg"
library.loc	character, location of library if local
n.upp	numeric, upper bound for number of genes in gene sets
n.low	numeric, lower bound for number of genes in gene sets
sets	character, GO or KEGG categories

Value

a list:

I	Indicator matrix of genes (rows) and gene sets (columns), for gene sets of size n, where n.low <= n <= n.upp
y	Indicator vector of genes in gene sets that are in 'idlist'
edge	data.frame of edges between genes and gene sets

Author(s)

Aimee Teo Broman

See Also

sequentialRM ILP bpList

Examples

library(org.Hs.eg.db)
## idlist <- sample(mappedRkeys(org.Hs.egSYMBOL),1000)

## out <- gs2edge(idlist,n.upp=30,idtype="SYMBOL",lib="org.Hs.eg")

## For input to sequentialRM:
## I=out$I
## y=out$y

## For input to bp:
## whole=colnames(out$I)
## part=out$y
## edge=out$edge

wiscstatman/Rolemodel documentation built on May 4, 2019, 6:32 a.m.