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

In phylter: Detect and Remove Outliers in Phylogenomics Datasets

Median normalization of 2D matrix by row or by colomn

Description

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.

Usage

normalize(mat, what = "none")

Arguments

mat

A matrix

what

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.

Value

A normalized matrix

Examples

# random matrix
x<-matrix(rnorm(270), nrow=9, ncol=14)

# normalize by row
x1<-normalize(x, "genes")

# normalize by column
x2<-normalize(x, "species")

phylter documentation built on Aug. 24, 2023, 9:10 a.m.