Description Usage Arguments References See Also
A method for computing Broad CMAP connectivity scores. This method is a kind of gene set enrichment analysis, it's initially designed for microarray samples, but could also applied to RNA-seq data. To use this method, we need a expression matrix and two corresponding gene sets.
| 1 | connectivity_score(data.matrix, id.up, id.down)
 | 
| data.matrix | the gene expression matrix | 
| id.up | first gene set, usually the up-regulated genes in a cell line | 
| id.down | second gene set, usually the down-regulated genes in a cell line | 
http://portals.broadinstitute.org/cmap/help_topics_linkified.jsp#connectivity score
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