neibMat: Create the neighbourhood matrix

In MalathiSIDona/pathDESeq: Pathway-Based Differential Expression Analysis for RNA-Seq Data

Description

Function will create an adjacent matrix for a given list of genes based on the first order interaction information retrieved from gene interaction databases (e.g., BioGRID interaction database).

Usage

neibMat(pathway.genes,interactions)

Arguments

pathway.genes	A vector of gene names considered for the analysis
interactions	A data frame contains gene interaction information. Column 1 represents the official gene symbol for interacting partner A. Column 2 represents the official gene symbol for interacting partner B. Each row is a gene-gene interaction pair.

Details

This function retrieves the available gene interaction information for a given list of genes and creates an adjacent list with all possible gene-gene interaction pairs. This function uses adj2mat function from the ENA R package as an internal function to create the neighbourhood matrix based on created adjacent list. The pathDESeq package uses this function as a internal function for the pgbmrfICM function.

Value

A matrix with 0's and 1's representing the neighbourhood information for the given gene set. For a particular gene its neighbouring genes will have value 1 and non-neighbouring genes will have value 0. The gene it self is considered as a neighbour with value 1. For a given gene list with n number of genes neibMat will return a n by n matrix with all 0's and 1's.

This function will save the created neighbourhood matrix as "neib_matrix.txt" in your working directory.

References

Chatr-Aryamontri, A., Breitkreutz, B.J., Oughtred, R., Boucher, L., Heinicke, S., Chen, D., Stark, C., Breitkreutz, A., Kolas, N., O'Donnell, L., et al.(2015). The BioGRID interaction database: 2015 update. Nucleic Acids Res.43:D470-D478

Jeffrey, D.A., & Guanghua, X. (2014). ENA:Ensemble Network Aggregation R package version 1.3-0.

Stark, C., Breitkreutz, B. J., Reguly, T., Boucher, L., Breitkreutz, A., & Tyers, M. (2006). BioGRID: a general repository for interaction datasets. Nucleic acids research, 34(suppl 1), D535-D539.

See Also

Reactome6.Hs, BioGRID.table, pgbmrfICM

Examples

#load pathway genes list
data("Reactome6.Hs")
head(Reactome6.Hs)
Reactome6.Hs<-as.character(Reactome6.Hs)

#Here we use BioGRID gene interaction information
#A data frame with 270,970 rows with 2 columns.
#"Gene.1"=Official gene symbol for interacting partner A
#"Gene.2"=Official gene symbol for interacting partner B
data("BioGRID.table")

#create neighbourhood matrix
neib.matrix<-neibMat(pathway.genes=Reactome6.Hs,interactions=BioGRID.table)

MalathiSIDona/pathDESeq documentation built on May 8, 2019, 3:37 p.m.