simplify

object


This convenience function takes an indexed <code><a rd-options="" href="/link/propr?package=propr&version=2.0.1" data-mini-rdoc="propr::propr">propr</a></code> object and
 subsets the object based on that index. In addition, it populates
 the <code>@pairs</code> slot of the new object with an updated version
 of the original index.


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.

Thomas Quinn

propr

Calculating Proportionality Between Vectors of Compositional
Data

simplify function


This convenience function takes an indexed <code><a rd-options='' href='propr'>propr</a></code> object and
 subsets the object based on that index. In addition, it populates
 the <code>@pairs</code> slot of the new object with an updated version
 of the original index.


simplify: Simplify Indexed Matrix

Description

Usage

Arguments

Value