distGO: Compare semantic similarity of GO.

In jtlovell/limmaDE2: A pipeline for differential expression analyses in LIMMA

Description

distGO A wrapper for GOSemSim::mgoSim, where similarity among GO terms stored in a list are returned as a matrix

Usage

distGO(go.list, n = 10, ont = "BP", organism = "arabidopsis",
  measure = "Wang", combine = "rcmax", verbose = TRUE,
  calc.distance = TRUE)

Arguments

go.list	A named list, where each element stores a character vector of GO ids. GO terms should be sorted so that the most important are first.
n	The number of GO terms to evaluate from the begining of the vector.
ont	The ontology type: one of "MF", "BP", and "CC" subontologies to be passed to mgoSim
organism	Organism with GO database, to be passed to mgoSim
measure	Measure of similarity to be passed to mgoSim
combine	Measure of combining similarity to be passed to mgoSim
verbose	Should updates be printed to the console?
calc.distance	Should a distance matrix (default) or a similarity matrix be returned.
...	Not currently in use

Details

More here soon.

Value

a matrix of (dis)similiarities

Examples

## Not run: 
more here soon

## End(Not run)

jtlovell/limmaDE2 documentation built on May 20, 2019, 3:14 a.m.