neib1065: Neighbourhood matrix for 1065 genes

Description Usage Format Details References See Also

Description

An example neighbourhood matrix for 1065 selected genes from Reactome pathways. This is a matrix with 0's and 1's representing the neighbourhood information for the given gene set.

Usage

1
data("neib1065")

Format

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 1065 genes the neib.matrix is a 1065x1065 matrix with all 0's and 1's while 1 represents neighbours and 0 represents non-neighbours

Details

This is an example neighbourhood matrix created using neibMat function in pathDESeq package to use as an input for estDE function. The neighbourhood information was retrieved from the BioGRID database.

References

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.,(2015). BioGRID: A General Repository for Interaction Datasets.

See Also

neibMat,estDE


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