getAdjacency

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

object

This argument indicates the value at which to
cutoff the results. For "rho" and "cor", the function
returns pairs with a value greater than the cutoff.
For "theta", "phi", and "phs", the function returns pairs
with a value less than the cutoff. Leave the argument as
<code>NA</code> to return all results.

cutoff

This argument indicates which features by
name should belong to a pair for that pair to get included
in the results. Subset performed by
<code>Partner %in% subset | Pair %in% subset</code>.

include

A boolean. If <code>FALSE</code>, <code>include</code> subsets
by <code>Partner %in% subset &amp; Pair %in% subset</code>.

This function uses <code>getNetwork</code> to
 return a <code>propr</code> or <code>propd</code>
 object as an adjacency matrix.
 The diagonal is set to 0.

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.

getAdjacency: Get Object as Adjacency Matrix

Description

Usage

Arguments

Value