plotCheck

A <code>propr</code> object created from <code>perb</code>.
However, <code>smear</code>, <code>dendrogram</code>, and <code>cytescape</code> will
also accommodate results from <code>phit</code> and <code>phis</code>.

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

Toggles whether to perform checks for an
"index-naive" plot function.

indexNaive

Performs data checks before plotting, triggering messages
 or errors when appropriate. For back-end use only.

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.

plotCheck: Plot Check

Description

Usage

Arguments

Value