GoMiner (version 1.2)

GOheatmap: GOheatmap

Description

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

Usage

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

Value

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

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

Examples

if (FALSE) {
# 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)
}