SetRank (version 1.1.0)

createPathwayTable: Creates a table of all significant pathways in different conditions.

Description

Creates a table of all significant pathways in different conditions.

Usage

createPathwayTable(networkList, setCollection)

Arguments

networkList

A list of SetRank networks created using the same set collection.

setCollection

The set collection used to perform the SetRank analysis.

Value

A data frame with column names being the names of the networks in the networkList argument and the rownames gene set IDs. The cells contain the adjusted p-values of each gene set in each network. When a gene set is not present in a network, the p-value will be set to 1. Two additional columns called "description" and "score" are added. The former is simply the description of the gene set. The latter is a score which attempts to reflect the importance of a gene set across the difference networks. The higher the score, the more important the network. This score is a combination of the number of networks where the gene set is observed and the geometric mean of the p-values of that set in these networks.