Description Usage Format Details References See Also
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.
1 | data("neib1065")
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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
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.
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.
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