|
A function to map from integer offsets in an array to the corresponding values of the row and column names. There is probably a better way but I didn't find it.
● Data Source:
BioConductor
● Keywords: manip
● Alias: idx2dimnames
●
0 images
|
|
The directed acyclic graph (DAG) based on finding the most specific terms for the supplied Entrez Gene IDs is constructed and returned. The constructuion is per GO ontology (there are three, MF, BP and CC) and once the most specific terms have been identified then all less specific terms are found (these are the parents of the terms) and then their parents and so on, until the root is encountered.
● Data Source:
BioConductor
● Keywords: manip
● Alias: makeGOGraph
●
0 images
|
notConn
(Package: GOstats) :
Find genes that are not connected to the others.
A function that takes as input a distance matrix and finds those entries that are not connected to any others (ie. those with distance Inf.
● Data Source:
BioConductor
● Keywords: manip
● Alias: notConn
●
0 images
|
oneGOGraph
(Package: GOstats) :
Construct the GO graph given a set of leaves.
Given one or more GO identifiers (which indicate the leaves in the graph) and a set of mappings to the less specific sets of nodes this function will construct the graph that includes that node and all children down to the root node for the ontology.
● Data Source:
BioConductor
● Keywords: manip
● Alias: GOGraph, oneGOGraph
●
1 images
|
probeSetSummary
(Package: GOstats) :
Summarize Probe Sets Associated with a hyperGTest Result
Given the result of a hyperGTest run (an instance of GOHyperGResult), this function lists all Probe Set IDs associated with the selected Entrez IDs annotated at each significant GO term in the test result.
● Data Source:
BioConductor
● Keywords: htest, manip
● Alias: probeSetSummary
●
0 images
|
|
The shortest path analysis was proposed by Zhou et. al. The basic computation is to find the shortest path in a supplied graph between two Entrez Gene IDs. Zhou et al claim that other genes annotated along that path are likely to have the same GO annotation as the two end points.
● Data Source:
BioConductor
● Keywords: manip
● Alias: shortestPath
●
0 images
|
simLL
(Package: GOstats) :
Functions to compute similarities between GO graphs and also
Both simUI and simLP compute a similarity measure between two GO graphs. For simLL, first the induced GO graph for each of its arguments is found and then these are passed to one of simUI or simLP.
● Data Source:
BioConductor
● Keywords: manip
● Alias: simLL, simLP, simUI
●
0 images
|
termGraphs
(Package: GOstats) :
Extraction and Plotting of GO Terms from a GOHyperGResult Object
These functions extract and plot graph instances representing the relationships among GO terms tested using hyperGTest.
● Data Source:
BioConductor
● Keywords: manip
● Alias: inducedTermGraph, plotGOTermGraph, termGraphs
●
0 images
|
These functions provide some tools for finding triads in an undirected graph. A triad is a clique of size 3. The function triadCensus returns a list of all triads.
● Data Source:
BioConductor
● Keywords: manip
● Alias: enumPairs, isTriad, reduce2Degreek, triad, triadCensus
●
0 images
|
|
This class represents the results of a test for overrepresentation of GO categories among genes in a selected gene set based upon the Hypergeometric distribution.
● Data Source:
BioConductor
● Keywords: classes
● Alias: GOHyperGResult-class, geneCounts,GOHyperGResult-method
●
0 images
|
providing 
.