PANDA (version 0.9.9)

SignificantSubcluster: Subclusters with KEGG annotations significantly enriched

Description

This function identifies subclusters whose members are significantly enrichment in certain KEGG pathways.

Usage

SignificantSubcluster(Dendrogram, Gene2Annotation, PPIdb, KGremove=TRUE,  SPoint=1, EPoint=9.7, p_value=0.001, ini.p_value=0.05)

Arguments

Dendrogram

An object in the class "dendrogram" returned from the function "ProteinCluster"

Gene2Annotation

A list that maps KEGG pathway ID to genes. The names should be gene symbols and the elements should be KEGG pathways. i.e.

$IGSF5

[1] "hsa04530" "hsa05120"

$OR2T8

[1] "hsa04740"

$hCG_1776980

[1] "hsa00020" "hsa00190" "hsa01100" "hsa05010" "hsa05012" "hsa05016"

......

PPIdb

A 2-column data frame consisting of binary interactions where each row i.e. c(A, B) represents an undirected edge (interaction) between gene A and gene B.

KGremove

If "TRUE", "hsa05200" and "hsa01100" will be excluded from KEGG-pathway based enrichment analysis as they are too broad.

SPoint

The starting point for searching for the KEGG-pathway enriched subclusters

EPoint

The endpoint for searching for the KEGG-pathway enriched subclusters

p_value

Description for p_value

ini.p_value

Description for ini.p_value

Value

This function identifies subclusters whose members are significantly enrichment in KEGG pathways and generate a dendrogram for these subclusters.

See Also

SignificantPairs, ProteinCluster, KEGGpredict, GOpredict