Description Usage Arguments Value Author(s)
Creates a table of all significant pathways in different conditions.
1 | createPathwayTable(networkList, setCollection)
|
networkList |
A list of SetRank networks created using the same set collection. |
setCollection |
The set collection used to perform the SetRank analysis. |
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.
Cedric Simillion
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