add_qvalue: Add a q-value column to any table with a p-value column

In DarwinAwardWinner/rctutils: Utility functions by Ryan C. Thompson

Add a q-value column to any table with a p-value column

Description

This function takes a results table and augments it with columns containing q-values and local FDR values computed using qvalue::qvalue()

Usage

add_qvalue(ttab, ...)

Arguments

ttab	A table of results produced by limma::topTable(), edgeR::topTags(), DESeq2::results(), or any table with a p-value column in it.
...	Additional arguments are passed to qvalue::qvalue().

Details

If a p-value column cannot be found or if the q-value computation fails, ttab will be returned with no new columns added, with a warning. This might happen if the p-value distribution is highly atypical, such that it is impossible to meaningfully estimate pi0.

Value

ttab possibly with two new columns added, named "QValue" and "LocFDR".

Examples

#TODO steal from topTable

DarwinAwardWinner/rctutils documentation built on July 22, 2022, 5:19 a.m.