proprPhit

A data.frame or matrix. A "count matrix" with subjects as rows and features as columns.

counts

A logical. If <code>TRUE</code>, forces symmetry by reflecting the "lower left triangle".

symmetrize

The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, this approach lacks statistical validity
when applied to relative data, including those biological count data produced by
microarray assays or high-throughput RNA-sequencing. Two metrics of proportionality,
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and
Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived from compositional
data analysis, a branch of math dealing specifically with relative data,
represent novel alternatives to correlation. This package introduces a programmatic
framework for the calculation of feature dependence through proportionality, as
discussed in the cited publications.

proprPhit: Calculate proportionality metric phi (Lovell 2015).

Description

Usage

Arguments

Value