GoMiner (version 1.2)

preprocessDB: preprocessDB

Description

driver to perform several preprocessing steps: quick peek trim small and large categories is the database for human species validate validated HGNC symbols in sampleList determine up to date (ie, contains GOGOA3$species) or legacy version of human database

Usage

preprocessDB(sampleList, GOGOA3, ontology, mn, mx, thresh, verbose)

Value

returns a list whose components are a trimmed version of GOGOA3 and (for human) a sampleList with validated HGNC symbols

Arguments

sampleList

character list of gene names

GOGOA3

return value of subsetGOGOA()

ontology

character string c("molecular_function", "cellular_component", "biological_process")

mn

integer param passed to trimGOGOA3, min size threshold for a category

mx

integer param passed to trimGOGOA3, max size threshold for a category

thresh

numerical paramter passed to checkGeneListVsDB()

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")
pp<-preprocessDB(cluster52,GOGOA3,"biological_process",20,200,0.5,3)
}