GOheatmap: GOheatmap

In GoMiner: Automate the Mapping Between a List of Genes and Gene Ontology Categories

GOheatmap

Description

generate a matrix to be used as input to a heat map

Usage

GOheatmap(sampleList, x, thresh, fdrThresh = 0.105)

Arguments

sampleList	character list of gene names
x	DB component of return value of GOtable3()
thresh	output of GOthresh()
fdrThresh	numeric value of FDR acceptance threshold

Value

returns a matrix to be used as input to a heat map

Examples

## Not run: 
# GOGOA3.RData is too large to include in the R package
# you can generate it using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO
#load("~/GODB_RDATA/GOGOA3.RData")
ONT<-"biological_process"
DB<-GOGOA3$ontologies[[ONT]]

#load("data/cluster52.RData")
sampleList<-cluster52

#load("data/x_thresh.RData")
heatmap<-GOheatmap(sampleList,DB,x_thresh)

## End(Not run)

GoMiner documentation built on April 12, 2025, 1:43 a.m.