run_the_tests: run_the_tests()

View source: R/21_run_the_tests.R

run_the_testsR Documentation

run_the_tests()

Description

Runs the specified enrichment test(s) and returns a table of results

Usage

run_the_tests(Query.miner, Universe.miner, test.type, general.select, subset.by,
  subset.select, enrich, pval, adjpval)

Arguments

Query.miner

list output from lipid.miner() function run on the Query dataset

Universe.miner

list output from lipid.miner() function run on the Universe dataset

test.type

character string specifying the type of enrichment test. Valid values are: "Fisher", "Binom", "Hyper", or "EASE".

general.select

vector of logical values of length ?, where the vector specifies ? in the following order ?

subset.by

character string specifying one of "category", "mainclass", or "subclass", which denote the ?

subset.select

vector of logical values of length ?, where the vector specifies ? in the following order ?

enrich

logical value specifying whether to ?

pval

numeric value specifying the pvalue (between 0 and 1) to use as a cutoff for the enrichment

adjpval

numeric value specifying a BH adjusted pvalue (between 0 and 1) to use as a cutoff for the enrichment

Author(s)

Geremy Clair, Kelly Stratton


PNNL-Comp-Mass-Spec/Rodin documentation built on Jan. 28, 2024, 2:12 a.m.