ratios

matrix

<p>A double. See vignette for details. Leave missing
to skip Box-Cox transformation.</p>

alpha

<p>The <code>ratios</code> function recasts a matrix with N feature columns
 as a new matrix with N * (N - 1) / 2 feature (log-)ratio columns.</p>

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

propr

Calculating Proportionality Between Vectors of Compositional
Data

David Lovell

Ionas Erb

Anders Bilgrau

Greg Gloor

Ryan Moore

ratios function

Recast Matrix as Feature (Log-)Ratios — ratios

Recast Matrix as Feature (Log-)Ratios

ratios: Recast Matrix as Feature (Log-)Ratios

Description

Usage

Arguments

Value

Details