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Last data update: 2014.03.03

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

goLeaves

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(mdgsa)


KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mdgsa/goLeaves.Rd_%03d_medium.png", width=480, height=480)
> ### Name: goLeaves
> ### Title: Keep just leaf nodes from the Gene Ontology DAG.
> ### Aliases: goLeaves
> ### Keywords: child go leaves terms
> 
> ### ** Examples
> 
> getGOnames (c ("GO:0006259", "GO:0006915", "GO:0043280"))
Using GO.db version: 3.3.0
                                                                                 GO:0006259 
                                                                    "DNA metabolic process" 
                                                                                 GO:0006915 
                                                                        "apoptotic process" 
                                                                                 GO:0043280 
"positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" 
> goLeaves   (c ("GO:0006259", "GO:0006915", "GO:0043280"))
Using GO.db version: 3.3.0
[1] "GO:0006259" "GO:0043280"
> 
> ## Not run: 
> ##D res <- uvGsa (rindex, goAnnotList)
> ##D goLeaves (res)
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>