splitOntologies: Split an annotation list of GO terms by ontologies.

In mdgsa: Multi Dimensional Gene Set Analysis.

Description

Splits an annotation list of GO terms according to the ontology to which each term belongs to.

Usage

splitOntologies(annot, na.rm = TRUE, verbose = TRUE)

Arguments

annot	annotation list.
na.rm	if TRUE 'unknown' terms are excluded.
verbose	verbose

Details

Uses the information form the library GO.db. If some id could not be associated to any ontology, they are returned in an unknown ontology named "missing".

Value

A list with tree components, one for each ontology. A fourth component is included is some term could not be allocated to any of the three GO ontologies.

Author(s)

David Montaner [e-mail]

See Also

propagateGO, goLeaves

Examples

getGOnames (c ("GO:0006915", "GO:0016020", "GO:0008152", "GO:0015288"))

annot <- list ("GO:0006915" = c ("g1"),
               "GO:0016020" = c ("g2", "g3"),
               "GO:0008152" = c ("g1", "g2", "g3"),
               "GO:0015288" = c ("g4", "g5"))
annot
splitOntologies (annot)

Example output

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

Using GO.db version: 3.4.1
         GO:0006915          GO:0016020          GO:0008152          GO:0015288 
"apoptotic process"          "membrane" "metabolic process"    "porin activity" 
$`GO:0006915`
[1] "g1"

$`GO:0016020`
[1] "g2" "g3"

$`GO:0008152`
[1] "g1" "g2" "g3"

$`GO:0015288`
[1] "g4" "g5"

Using GO.db version: 3.4.1
$bp
$bp$`GO:0006915`
[1] "g1"

$bp$`GO:0008152`
[1] "g1" "g2" "g3"


$cc
$cc$`GO:0016020`
[1] "g2" "g3"


$mf
$mf$`GO:0015288`
[1] "g4" "g5"

mdgsa documentation built on Nov. 8, 2020, 5:05 p.m.