normalize

This function normalizes the 2WR matrix (or any 2D matrix) according to the
species (rows) or to the genes (columns), by dividing each row or each column by its median.

Analyzis and filtering of phylogenomics datasets.
It takes an input either a collection of gene trees (then transformed to matrices) or directly a collection of gene matrices and performs an iterative process to identify
what species in what genes are outliers, and whose elimination significantly improves the concordance between the input matrices. The methods builds upon the Distatis approach (Abdi et al. (2005) <doi:10.1101/2021.09.08.459421>), a generalization of classical multidimensional scaling to multiple distance matrices.

Aurélie Siberchicot

phylter

Detect and Remove Outliers in Phylogenomics Datasets

Damien M. de Vienne

Stéphane Dray

Théo Tricou

normalize function

<dl><dt>mat</dt>
<dd>A matrix</dd>
<dt>what</dt>
<dd>Character string indicating whether the matrix should be
normalized and how. If what="none", the matrix is not normalized (the
default), if what="species", the matrix is normalized so that the difference
between species is increased, and if what="genes", the matrix is normalized
so that the difference between genes is increased. Normalization consists
in dividing either each row or each columns by its median.</dd></dl>

Arguments

Median normalization of 2D matrix by row or by colomn — normalize

<dl>

<dt>mat</dt>
<dd>A matrix</dd>


<dt>what</dt>
<dd>Character string indicating whether the matrix should be
normalized and how. If what="none", the matrix is not normalized (the
default), if what="species", the matrix is normalized so that the difference
between species is increased, and if what="genes", the matrix is normalized
so that the difference between genes is increased. Normalization consists
in dividing either each row or each columns by its median.</dd>

</dl>

normalize: Median normalization of 2D matrix by row or by colomn

Description

Usage

Value

Arguments

Examples