Description Usage Arguments Value Author(s) See Also Examples
Given a vector of genes and a gene set library, create input objects for enrichment functions
1 |
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 |
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 |
Aimee Teo Broman
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