propagateGO: Propagate Gene Ontology annotation.

In mdgsa: Multi Dimensional Gene Set Analysis.

Description

Genes annotated under a GO term inherit the annotation from all its ancestors.

Usage

propagateGO(annot, verbose = FALSE)

Arguments

annot	annotation list or matrix.
verbose	verbose

Details

Uses the library GO.db.

Value

A annotation matrix or list with the propagated annotation.

Author(s)

David Montaner [e-mail]

See Also

annotMat2list, annotFilter

Examples

mat <- cbind (c("gene1", "gene2"), c("GO:0034390", "GO:0042889"))
mat
propagateGO (mat)

li <- list ('GO:0034390' = "gene1", 'GO:0042889' = "gene2")
li
propagateGO (li)

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

     [,1]    [,2]        
[1,] "gene1" "GO:0034390"
[2,] "gene2" "GO:0042889"
      [,1]    [,2]        
 [1,] "gene1" "GO:0034390"
 [2,] "gene2" "GO:0042889"
 [3,] "gene1" "GO:0006915"
 [4,] "gene1" "GO:0008150"
 [5,] "gene1" "GO:0008219"
 [6,] "gene1" "GO:0009987"
 [7,] "gene1" "GO:0010657"
 [8,] "gene1" "GO:0012501"
 [9,] "gene2" "GO:0006810"
[10,] "gene2" "GO:0006811"
[11,] "gene2" "GO:0006820"
[12,] "gene2" "GO:0008150"
[13,] "gene2" "GO:0015711"
[14,] "gene2" "GO:0015718"
[15,] "gene2" "GO:0015849"
[16,] "gene2" "GO:0046942"
[17,] "gene2" "GO:0051179"
[18,] "gene2" "GO:0051234"
[19,] "gene2" "GO:0071702"
$`GO:0034390`
[1] "gene1"

$`GO:0042889`
[1] "gene2"

$`GO:0006810`
[1] "gene2"

$`GO:0006811`
[1] "gene2"

$`GO:0006820`
[1] "gene2"

$`GO:0006915`
[1] "gene1"

$`GO:0008150`
[1] "gene1" "gene2"

$`GO:0008219`
[1] "gene1"

$`GO:0009987`
[1] "gene1"

$`GO:0010657`
[1] "gene1"

$`GO:0012501`
[1] "gene1"

$`GO:0015711`
[1] "gene2"

$`GO:0015718`
[1] "gene2"

$`GO:0015849`
[1] "gene2"

$`GO:0034390`
[1] "gene1"

$`GO:0042889`
[1] "gene2"

$`GO:0046942`
[1] "gene2"

$`GO:0051179`
[1] "gene2"

$`GO:0051234`
[1] "gene2"

$`GO:0071702`
[1] "gene2"

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