proprPerb

<p>A data.frame or matrix. A "count matrix" with
subjects as rows and features as columns.</p>

counts

<p>A numeric scalar. Specifies reference feature(s)
for additive log-ratio transformation. The argument will also
accept feature name(s) instead of the index position(s).
Set to "iqlr" to use inter-quartile log-ratio transformation.
Ignore to use centered log-ratio transformation.</p>

ivar

The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, this approach lacks statistical validity
when applied to relative data. This includes, for example, biological count data
generated by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
ChIP-sequencing, Methyl-Capture sequencing, and other techniques. 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

proprPerb function

Calculate proportionality metric rho (Erb 2016). — proprPerb

Calculate proportionality metric rho (Erb 2016).

proprPerb: Calculate proportionality metric rho (Erb 2016).

Description

Usage

Arguments

Value