top.counts

<p>Includes the non-transformed count abundances from all
 cane toad transcripts with at least 10 counts in at least
 10 samples, subsetted to include only those indexed
 by <code>rho &gt; .995</code>. Used for vignette.</p>

datasets

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

top.counts function

<p>An object of class <code>matrix</code> with 20 rows and 409 columns.</p>

Format

Example propr Object — top.counts

Example propr Object

top.counts: Example propr Object

Description

Usage

Arguments

Format