goLeaves: Keep just leaf nodes from the Gene Ontology DAG.
In mdgsa: Multi Dimensional Gene Set Analysis.

Description Usage Arguments Details Value Author(s) See Also Examples

Cuts significant terms and filters out all redundant GO terms from a list of uvGsa results.

1 2	goLeaves(gsaout, cutoff = 0.05, pvalue = "padj", statistic = "lor", verbose = TRUE, sort = TRUE)

`gsaout`	data.frame; output from uvGsa.
`cutoff`	p-value cutoff for considering significant a Gene Set.
`pvalue`	p-value column to be used. Default is named "padj" as in uvGsa output.
`statistic`	name of the column containing the log odds ratio from the uvGsa analysis.
`verbose`	verbose
`sort`	if TRUE the output data.frame is ordered according to significance.

Uses the library GO.db to find the 'ancestors' of each GO term. Those ancestors are discarded form the uvGsa results.

Alternatively, the function may also take a character vector of GO ids in the gsaout parameter. In such case the function returns also a character vector of GO ids, containing just the GO terms being "leaves" of the original set.

The input data.frame but keeping just the 'significant' and 'non redundant' GO terms.

David Montaner dmontaner@cipf.es

uvGsa, uvPat, propagateGO, pval2index

getGOnames (c ("GO:0006259", "GO:0006915", "GO:0043280"))
goLeaves   (c ("GO:0006259", "GO:0006915", "GO:0043280"))

## Not run: 
res <- uvGsa (rindex, goAnnotList)
goLeaves (res)

## End(Not run)