pals

object

An integer. The maximum number of PALs to index
when calculating <code><a rd-options="" href="/link/pals?package=propr&version=3.1.8" data-mini-rdoc="propr::pals">pals</a></code> in the network.

This function finds the Popular Adjacent Ligand or Self (PALs)
 for each feature in the <code>@theta</code> slot of a <code>propd</code>
 object. Specifically, we define PALs as the adjacent node with
 the highest amount of connectivity. If node itself has more
 connectivity than any of its neighbors, it is its own PAL.

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

pals function

An integer. The maximum number of PALs to index
when calculating <code><a rd-options='' href='pals'>pals</a></code> in the network.

pals: Calculate PALs for Pairs

Description

Usage

Arguments

Value