allchains.cat: allchains.cat()

Description Usage Arguments Value Author(s) Examples

Description

Function to evaluate the specific chains enriched within each category

Usage

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allchains.cat(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

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PNNL-Comp-Mass-Spec/Rodin documentation built on May 31, 2019, 5:18 p.m.