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| coloredGraph-class | Class "coloredGraph" |
| colorNodes | attach node coloring information to a graphNEL instance |
| colorNodes,graphNEL,numeric,character,function-method | attach node coloring information to a graphNEL instance |
| graphcMAP | obtain a graph object corresponding to a cMAP pathway |
| plot,coloredGraph-method | Class "coloredGraph" |
| plot,pwayGraph-method | Class "pwayGraph" - extension to graphNEL for pathway rendering |
| plotExGraph | plot a gene network, coloring nodes according to relative expression values |
| pwayGraph-class | Class "pwayGraph" - extension to graphNEL for pathway rendering |
| pwayRendAttrs | Class "coloredGraph" |
| reduceES | collapse the assay values in an ExpressionSet to a set of specified genes, using a statistic when multiple probes map to a given gene |
| rendercMAPPathway | Render pathways from cMAP |