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 duplicating 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. As an alternative, Lovell
et al propose a proportionality metric, phi, derived from compositional data
analysis, a branch of math dealing specifically with relative data. In a
subsequent publication, Erb and Nicodemus expounded these efforts by elaborating
on another proportionality metric, rho. This package introduces a programmatic
framework for the calculation of feature dependence using proportionality and
other compositional data methods discussed in the cited publications.

proprPhit: Calculate proportionality metric phi (Lovell 2015).

Description

Usage

Arguments

Value