goStatTest: goStatTest

In Gibbsdavidl/ProCoNA: Protein co-expression network analysis (ProCoNA).

Description

Wrapper function to run the hyperGTest from package GOstats, after mapping each peptide to an entrez ID.

Usage

goStatTest(pnet, module, pepinfo, pepColName, protColName, universe, 
    onto, annot, pvalue, cond)

Arguments

pnet	Procona network object.
module	Module of interest (numeric)
pepinfo	The mass tag info, mapping peptides to proteins.
pepColName	Column name in mass tag info for peptides
protColName	Column name in mass tag info for proteins
universe	Table mapping protein IDs to entrez IDs
onto	The ontology catagory (bp etc)..
annot	The annotation database to use
pvalue	pvalue cutoff
cond	conditional parameter, see GOstats.

Value

Returns the results of the hyper geometric test.

Author(s)

David L Gibbs

Examples

## Not run: 
data(ProCoNA_Data)
#net1 <- buildProconaNetwork("peptide network", peptideData, pow=12)
goStatTest(net1, 1, masstagdb, "Mass_Tag_ID", "Reference", universe, "BP", "org.Mm.eg.db", 0.005, FALSE)

## End(Not run)

Gibbsdavidl/ProCoNA documentation built on May 8, 2019, 7:51 p.m.