Usage
doEnrichment(compSel, chip, onto, hgCutoff, cond, universe, path, db, pack.annot.EID, Slist, it, cutoff, entrez2symbol)
Arguments
compSel
A list containing three elements
- compSel
- the projection values of
contributing genes that were selected based on their
absolute projection
- compSel_neg
- the projection
values of contributing genes that have negative
projections
- compSel_pos
- the projection values of
contributing genes that have positive projections
chip
The annotation package
onto
A string specifying the GO ontology to use.
Must be one of 'BP', 'CC', or 'MF', see
GOHyperGParams.
Only used when argument db is 'GO'. hgCutoff
The p-value threshold
cond
A logical indicating whether the calculation
should conditioned on the GO structure, see
GOHyperGParams. path
The path where results will be saved
db
The used database to use ('GO' or 'KEGG')
pack.annot.EID
The name of the environment of the
annotation package containing the annotation for Entrez
Gene.
Slist
The list of gene projections across all
components
it
The index of the component
cutoff
The threshold applied on the gene
projections, used to select the contributing genes
entrez2symbol
A vector of all gene Symbols
involved in the analysis indexed by their Entrez Gene
IDs. It is only used when annotation(params) is
empty, and allows to associate gene sets to Symbols.