This function writes four files that are used to build an network using Cytoscape and the EnrichmentMap app. 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 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 scores
prepareCytoscape(terms, gmt, file_dir, col.significance)a data.table with columns 'term.id', 'term.name', 'adjusted.p.val'
an abridged gmt object containing only the pathways that were found to be significant
user defined directory to write output files
a data.table with a column 'term.id' and a column for each test indicating whether a pathway is signficiant (TRUE) or not (FALSE) when considering only that column. If contribution==TRUE, use col.significance=NULL and this will be skipped
None