This function writes four text files that are used to build an network using
Cytoscape and the EnrichmentMap app. The files are prefixed with
The four files written are:
A list of significant terms and the
associated p-value. Only terms with
adjusted.p.val <= significant are
written to this file
A matrix indicating whether the significant
pathways are found to be significant when considering only one column (i.e., type of omics evidence) from
scores. A 1 indicates that that term is significant using only that
column to test for enrichment analysis
A shortened version of the supplied GMT file, containing only the terms in pathways.txt.
A legend with colours matching contributions
from columns in
A data.table object with the columns 'term.id', 'term.name', 'adjusted.p.val'.
An abridged GMT object containing only the pathways that were found to be significant in the ActivePathways analysis.
The user-defined file prefix and/or directory defining the location of the files.
A data.table object with a column 'term.id' and a column
for each type of omics evidence indicating whether a term was also found to be signficiant or not
when considering only the genes and p-values in the corresponding column of the
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