goLeaves {mdgsa} | R Documentation

## 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.

### 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.

### Value

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

### Author(s)

David Montaner dmontaner@cipf.es

### 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)

[Package mdgsa version 1.14.0 Index]