get_parent_nodes: Get all parent nodes of gene ontology categories
In GOfuncR: Gene ontology enrichment using FUNC

Description Usage Arguments Details Value Author(s) References See Also Examples

Returns all parent nodes (higher level categories) of GO-categories given their GO-IDs, e.g. c('GO:0042254', 'GO:0000109'). The output also states the shortest distance to the parent node. Note that a GO-ID itself is also considered as parent with distance 0.

1	get_parent_nodes(go_ids, term_df = NULL, graph_path_df = NULL, godir = NULL)

`go_ids`	a character() vector of GO-IDs, e.g. c('GO:0051082', 'GO:0042254').
`term_df`	optional data.frame() with an ontology 'term' table. Alternative to the default integrated GO-graph or `godir`. Also needs `graph_path_df`.
`graph_path_df`	optional data.frame() with an ontology 'graph_path' table. Alternative to the default integrated GO-graph or `godir`. Also needs `term_df`.
`godir`	optional character() specifying a directory that contains the ontology tables 'term.txt' and 'graph_path.txt'. Alternative to the default integrated GO-graph or `term_df` + `graph_path_df`.

By default the package's integrated GO-graph is used, but a custom ontology can be defined, too. For details on how to use a custom ontology with term_df + graph_path_df or godir please refer to the package's vignette. The advantage of term_df + graph_path_df over godir is that the latter reads the files 'term.txt' and 'graph_path.txt' from disk and therefore takes longer.

a data.frame() with four columns: child GO-ID (character()), parent GO-ID (character()), parent GO-name (character()) and distance (numeric()).

Steffi Grote

[1] Ashburner, M. et al. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics 25, 25-29.

get_names
get_child_nodes

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## get the parent nodes (higher level GO-categories) of two random GO-IDs
parents = get_parent_nodes(c('GO:0051082', 'GO:0042254'))
parents

Loading required package: vioplot
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Warning message:
no DISPLAY variable so Tk is not available 
   child_go_id parent_go_id                                   parent_name
1   GO:0042254   GO:0042254                           ribosome biogenesis
2   GO:0042254   GO:0022613          ribonucleoprotein complex biogenesis
3   GO:0042254   GO:0044085                 cellular component biogenesis
4   GO:0042254   GO:0071840 cellular component organization or biogenesis
5   GO:0042254   GO:0009987                              cellular process
6   GO:0042254   GO:0008150                            biological_process
7   GO:0051082   GO:0051082                      unfolded protein binding
8   GO:0051082   GO:0005515                               protein binding
9   GO:0051082   GO:0005488                                       binding
10  GO:0051082   GO:0003674                            molecular_function
   distance
1         0
2         1
3         2
4         3
5         4
6         5
7         0
8         1
9         2
10        3