mdgsa (version 1.2.0)

goLeaves: Keep just leaf nodes from the Gene Ontology DAG.

Description

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

Usage

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

Arguments

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.

Value

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

Details

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.

See Also

uvGsa, uvPat, propagateGO, pval2index

Examples

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)