list2score: Create a score vector from a list of genes

In atbroman/allez: Random-set calibration of gene-set statistics

Description

Given a list of genes, a platform (chip type or organism), and GO or KEGG category, create a binary vector for input into allez

Usage

list2score(idlist, lib, idtype = c("SYMBOL", "ENTREZID", "PROBEID", "REFSEQ", "ENSEMBL", "ACCNUM", "UNIPROT", "PMID"),sets=c("ALL","GO","KEGG"))

Arguments

idlist	character vector of gene symbols, entrez ID, probe ID (for chip platform only), Refseq ID, Ensembl ID, Accession number, Uniprot ID, or PMID.
lib	character string, name of data package corresponding to microarray platform or organism (e.g. "hgu133plus2" or "org.Hs.eg", do not include ".db")
idtype	character string, one of "SYMBOL", "ENTREZID", "PROBEID", "REFSEQ", "ENSEMBL", "ACCNUM", "UNIPROT", or "PMID"
sets	character string, gene set to be used: "ALL", "GO" or "KEGG". If "ALL", all EG or PROBE IDs in platform/organism. If "GO" or "KEGG" all EG or PROBE IDsin geneset.

Value

Named numeric vector of 0,1, with names corresponding to all probe_id on the platform or gene_id in the organism database.

Author(s)

Aimee Teo Broman

See Also

allez

Examples

library(hgu133plus2.db)
idlist <- sample(mappedRkeys(hgu133plus2SYMBOL),500)

scores <- list2score(idlist,lib="hgu133plus2",idtype="SYMBOL",sets="GO")

atbroman/allez documentation built on May 10, 2019, 2:08 p.m.