complexStatus {PCpheno}R Documentation

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)

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 CoHyperG function)

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

Author(s)

N. LeMeur

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)

[Package PCpheno version 1.4.1 Index]