pd.d

Includes results from <code><a rd-options="" href="/link/propd?package=propr&version=3.1.8" data-mini-rdoc="propr::propd">propd</a></code> as applied to
 cane toad transcripts with at least 40 counts in at least
 20 samples (after removing any transcripts with 0 counts).
 The resultant object is filtered to include only the top
 1000 theta_d values in the <code>@theta</code> slot.

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

pd.d function

An object of class <code>propd</code> of length 1.

Format

Includes results from <code><a rd-options='' href='propd'>propd</a></code> as applied to
 cane toad transcripts with at least 40 counts in at least
 20 samples (after removing any transcripts with 0 counts).
 The resultant object is filtered to include only the top
 1000 theta_d values in the <code>@theta</code> slot.

pd.d: Example propd Object

Description

Usage

Arguments

Format