proprALR

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

A numeric scalar. Specificies feature to use as reference for additive log-ratio transformation.

ivar

A logical. If TRUE, function first checks for negative and NA values.

check

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.

proprALR: Calculates the additive log-ratio transformation.

Description

Usage

Arguments

Value