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, verbose)

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
verbose	integer vector representing classes

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
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# you can generate it using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/tree/main/databases
load("/Users/barryzeeberg/personal/GODB_RDATA/goa_human/GOGOA3_goa_human.RData")
heatmap<-GOheatmap(cluster52,GOGOA3$ontologies[["biological_process"]],x_thresh,verbose=1)

## End(Not run)

GoMiner documentation built on June 8, 2025, 1:29 p.m.