ibh-package: Interaction Based Homogeneity

In ibh: Interaction Based Homogeneity for Evaluating Gene Lists

Description

This package contains methods for evaluating Interaction Based Homogeneity for lists of genes. Given a gene list of n genes, we first form an adjacency matrix A whose rows and columns are genes in the list where

A_{ij} = 1

if genes i and j have an interaction in the network and

A_{ij}=0

otherwise. The Interaction Based Homogeneity for a gene list

L=\{g_1, g_2, ..., g_n\}

of size n is then calculated as:

InteractionBasedHomogeneity(L) ={{∑_{i=1}^n∑_{j=1}^n{A_{ij}}}\over{n^2}}

Details

Package:	ibh
Type:	Package
Version:	1.0.0
Date:	2011-01-19
License:	GPL (version 2 or newer)
LazyLoad:	yes

The user can provide his own interaction list or can use predefined gene lists which are created based on the BioGRID Interactions. Both gene lists and result of clustering methods such as kmeans or hclust can be used as inputs. Entrez identifiers, unique ids (systematic names) or official names can be used as gene/protein identifiers.

Author(s)

Kircicegi Korkmaz <[e-mail]>, Volkan Atalay <[e-mail]>, Rengul Cetin-Atalay <[e-mail]>

Maintainer: Kircicegi Korkmaz <[e-mail]>

References

Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9

Examples

	require(simpIntLists)
	data(ArabidopsisBioGRIDInteractionEntrezId)
	listofGeneList <- list(list(839226,817241, 824340, 832179, 818561, 831145, 838782, 826404), 
					list( 832018, 839226, 839226, 838824));
	ibhForMultipleGeneLists(ArabidopsisBioGRIDInteractionEntrezId, 
			listofGeneList)

	require(simpIntLists)
	listofGeneList <- list(list(839226,817241, 824340, 832179, 818561, 831145, 838782, 826404), 
list( 832018, 
				839226, 839226, 838824));
	ibhForMultipleGeneListsBioGRID(listofGeneList, 
				 organism="arabidopsis",
				 idType = "EntrezId");
	listofGeneList <- list(list("YJR151C", "YBL032W",   "YAL040C",   "YBL072C",   "YCL050C",
					   "YCR009C"), 
				list("YDR063W", "YDR074W", "YDR080W", "YDR247W", "YGR183C", "YHL033C"), 
				list("YOL068C" , "YOL015W" ,  "YOL009C" ,  "YOL004W" ,  "YOR065W"  ));
	ibhForMultipleGeneListsBioGRID(listofGeneList, organism="yeast", 
			idType = "UniqueId");


	require(yeastCC)
	require(stats)
	data(yeastCC)
	subset <- exprs(yeastCC)[1:50,]
	d <- dist(subset,method="euclidean")
	k <- kmeans(d, 3);
	ibhClusterEvalBioGRID(k$cluster, rownames(subset),
			organism="yeast", idType="UniqueId")

ibh documentation built on Nov. 8, 2020, 7:49 p.m.