updateCutoffs

A <code>propr</code> or <code>propd</code> object.

object

For <code>updateCutoffs</code>, a numeric vector.
this argument provides the FDR cutoffs to test.
For graph functions, a numeric scalar. This argument
indicates the maximum theta to include in the figure.
For graph functions, a large integer will instead
retrieve the top N pairs as ranked by theta.

cutoff

An integer. The number of parallel cores to use.

ncores

This function updates FDR for a set of cutoffs.

The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. This package implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.

Thomas Quinn

updateCutoffs: Update FDR by Permutation

Description

Usage

Arguments

Value

Details