SignificantSubcluster-methods: Subclusters with KEGG annotations significantly enriched

In PANDA: Preferential Attachment Based Common Neighbor Distribution Derived Functional Associations

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

PANDA documentation built on May 2, 2019, 6:53 a.m.