allchains.sub: allchains.sub()

In PNNL-Comp-Mass-Spec/Rodin: Lipid Mini-on

allchains.sub()

Description

Function to evaluate the specific chains enriched within each sub class

Usage

allchains.sub(X, Y, test = "Fisher", enrich = FALSE, pval = 0.05,
  adjpval = 1, TGcollapse.rm = TRUE)

Arguments

X	has to be a <Query>.intact object that was created using the lipid.miner function
Y	has to be your <Universe>.intact object that was created using the lipid.miner function
test	has to be a type of test in the list "Fisher", "Binom", "Hyper", or "EASE"
enrich	TRUE or FALSE (FALSE by default) to choose between showing all the results of the test or only the enriched ones based on a pvalue
pval	regular pvalue cutoff (0.05 by default)
adjpval	BH adjusted pvalue cutoff (1.0 by default)
TGcollapse.rm	Boolean to indicate if the collapsed TG need to be removed (default TRUE)

Value

This function will return a data.frame containing the tested classifiers (rows), the counts and percentage of identifiers/chains falling in this classifier, a binom.test() pvalue, a BH corrected pvalue and a fold change

Author(s)

Geremy Clair

Examples

allchains.sub(queryExample.intact,universeExample.intact,test="Hyper",enrich=TRUE, p=0.05)

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