calculateTheta

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

counts

A character vector. Group or sub-group memberships,
ordered according to the row names in <code>counts</code>.

group

A double. See vignette for details. Leave missing
to skip Box-Cox transformation.

alpha

A numeric vector. A vector of pre-computed
log-ratio variances. Optional parameter.

A character string. The name of the theta
type to return if only calculating one theta type.
Used to make <code>updateCutoffs</code> faster.

only

A boolean. Toggles whether to calculate
theta using <code>limma::voom</code> weights.

weighted

A matrix. Pre-computed <code>limma</code>-based
weights. Optional parameter.

weights

Calculate differential proportionality measure, theta.
 Used by <code><a rd-options="" href="/link/propd?package=propr&version=3.1.9" data-mini-rdoc="propr::propd">propd</a></code> to build the <code>@theta</code>
 slot. A numeric <code>alpha</code> argument will trigger
 the Box-Cox transformation.

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

calculateTheta function

Calculate differential proportionality measure, theta.
 Used by <code><a rd-options='' href='propd'>propd</a></code> to build the <code>@theta</code>
 slot. A numeric <code>alpha</code> argument will trigger
 the Box-Cox transformation.

calculateTheta: Calculate Theta

Description

Usage

Arguments

Value