slate

A <code>propr</code> or <code>propd</code> object.

An integer. For <code>propr</code> methods, the number
of co-clusters (where all pairs receive a specified color
if and only if both members belong to same the cluster).
For <code>propd</code> methods, the maximum number of PALs to index
when calculating <code><a rd-options="" href="/link/pals?package=propr&version=4.2.6" data-mini-rdoc="propr::pals">pals</a></code> in the network.

A logical scalar. Set to <code>FALSE</code> to disable
the courtesy prompt when working with big data.

prompt

A logical scalar. Set to <code>TRUE</code> to produce
a dynamic plot using the <code>plotly</code> package.

plotly

Builds a table of VLR, VLS, and proportionality
 for each feature pair in a <code>propr</code> object. If the
 argument <code>k</code> is provided, the table will also
 include co-cluster membership.
 Returns a <code>data.frame</code> of all pairwise relationships.
 If the argument <code>k</code> is provided, returns a list of
 the <code>data.frame</code> of pairwise relationships and the
 cluster membership.

The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. 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

Ryan Moore

slate function

An integer. For <code>propr</code> methods, the number
of co-clusters (where all pairs receive a specified color
if and only if both members belong to same the cluster).
For <code>propd</code> methods, the maximum number of PALs to index
when calculating <code><a rd-options='' href='pals'>pals</a></code> in the network.

slate: Build `propr` Results Table

Description

Usage

Arguments