PCpheno (version 1.34.0)

complexStatus: Complex Status

Description

Categorize the complex whether or not a complex is composed of a significant number of genes involved in a particular phenotype than expected by chance.

Usage

complexStatus(data, phenotype, interactome, threshold=0.05)

Arguments

data

Output from CoHyperG test

phenotype

List of gene names inducing an observed phenotype, e.g., list of essential gene names (see package SLGI)

interactome

A binary matrix composed of genes (rows) and biological complexes (columns) (see package ScISI)

threshold

pvalue threshold (default 0.05)

Value

The returned value is a list with components:

A

"interesting" complexes, complexes with a significant number of interesting genes, i.e., genes that participate to a particular phenotype (at a given p-values threshold)

B

complexes with a NON significant number of interesting genes BUT that SHARE genes with complexes from the A status

C

complexes with a NON significant number of interesting genes AND that DON'T SHARE interesting genes with complexes from cat A

D

complexes WITHOUT interesting genes, i.e. the one involved in the studied phenotype

Details

We form four distinct categories from A to D to characterize how a complex might be involved in a particular phenotype (according to the number of genes it contains and that are involved in a particular phenotype - see also hyperGTest function)

Examples

data(ScISI)
data(essglist)
essential <- names(essglist)

CoparamsESS <- new("CoHyperGParams",
                   geneIds=essential, 
                   universeGeneIds=rownames(ScISI),
                   annotation="org.Sc.sgd.db",
                   categoryName="ScISI",
                   pvalueCutoff=0.01,
                   testDirection="over")

sign<- hyperGTest(CoparamsESS)
test05 <-complexStatus(data=sign, phenotype=essential,
interactome=ScISI, threshold=0.05)