trimGOGOA3: trimGOGOA3

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

trimGOGOA3

Description

remove categories from GOGOA3 that are too small or too large

Usage

trimGOGOA3(GOGOA3, mn, mx, verbose)

Arguments

GOGOA3	return value of subsetGOGOA()
mn	integer min size threshold for a category
mx	integer max size threshold for a category
verbose	integer vector representing classes

Details

If a category is too small, it is unreliable for statistical evaluation Also, in the extreme case of size = 1, then that category is essentially equivalent to a gene rather than a category. Same is partially true for size = 2. If a category is too large, it is too generic to be useful for categorization. Finally, by trimming the database, analyses will run faster.

Value

returns trimmed version of GOGOA3

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.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/tree/main/databases

GOGO3tr<-trimGOGOA3(GOGOA3,mn=2,mx=200,1)

## End(Not run)

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