| Title: | graph support for KO, KEGG Orthology |
|---|---|
| Description: | graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs. |
| Authors: | VJ Carey <[email protected]> |
| Maintainer: | VJ Carey <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 2.59.0 |
| Built: | 2024-11-07 05:59:32 UTC |
| Source: | https://github.com/bioc/keggorthology |
obtain probe set IDs associated with a KO term
getKOprobes(str, useAcc=TRUE, plat="hgu95av2", na.action=na.omit)getKOprobes(str, useAcc=TRUE, plat="hgu95av2", na.action=na.omit)
str |
string giving a KEGG orthology term |
useAcc |
logical – use all accessible terms? |
plat |
platform corresponding to a bioconductor annotation package, e.g., hgu95av2.db |
na.action |
function for dealing with NA |
Based on keggorthology read of KEGG orthology, March 2 2010.
Specifically, we run wget on
ftp://ftp.genome.jp/pub/kegg/brite/ko/ko00001.keg and use parsing
and modeling code given in inst/keggHTML to generate a data frame
respecting the hierarchy, and then keggDF2graph to
construct the graph.
Looks up the requested term and gives back the unique probe set ids on the platform.
character vector, typically processed by na.omit
Vince Carey <[email protected]>
getKOtags("insulin") es = graph::acc(KOgraph, "Endocrine System") nm = names(es[[1]]) nm esp = lapply(nm, getKOprobes) names(esp) = nm sapply(esp, length)getKOtags("insulin") es = graph::acc(KOgraph, "Endocrine System") nm = names(es[[1]]) nm esp = lapply(nm, getKOprobes) names(esp) = nm sapply(esp, length)
indented textual rendering of nodes of a hierarchical graph
indRender(klike, from=nodes(klike)[1], indent=" ")indRender(klike, from=nodes(klike)[1], indent=" ")
klike |
a graph, with tree structure similar to |
from |
a node name from which the rendering should proceed to all leaves |
indent |
token to use for indentation – will be replicated to depth of node to be rendered to its left |
Based on keggorthology read of KEGG orthology, March 2 2010.
Specifically, we run wget on
ftp://ftp.genome.jp/pub/kegg/brite/ko/ko00001.keg and use parsing
and modeling code given in inst/keggHTML to generate a data frame
respecting the hierarchy, and then keggDF2graph to
construct the graph.
NULL
Vince Carey <[email protected]>
data(KOgraph) indRender(KOgraph, "Human Diseases")data(KOgraph) indRender(KOgraph, "Human Diseases")
create a graph from a specific data frame format for KEGG orthology
keggDF2graph(df, root="KO.June07root") data(KOgraph)keggDF2graph(df, root="KO.June07root") data(KOgraph)
df |
the data frame |
root |
a name for root node |
the obvious directed graph structure from root to leaf nodes (pathway names) is instantiated for the orthology, nodeData attribute tag is loaded with the numerical tag for the term in KEGG, and nodeData attribute depth is loaded with depth from root
Based on keggorthology read of KEGG orthology, March 2 2010.
Specifically, we run wget on
ftp://ftp.genome.jp/pub/kegg/brite/ko/ko00001.keg and use parsing
and modeling code given in inst/keggHTML to generate a data frame
respecting the hierarchy, and then keggDF2graph to
construct the graph.
a graphNEL-class instance
This is only a support function. The graph is serialized in the package data directory.
Vince Carey <[email protected]>
data(keggOrthDF) keggOrthDF[1:5,] data(KOgraph) graph::nodes(KOgraph)[1:4] graph::nodeData(KOgraph,,"tag")[1:5] graph::nodeData(KOgraph,,"depth")[1:5]data(keggOrthDF) keggOrthDF[1:5,] data(KOgraph) graph::nodes(KOgraph)[1:4] graph::nodeData(KOgraph,,"tag")[1:5] graph::nodeData(KOgraph,,"depth")[1:5]