Function reference • phylter

All functions

Dist2WR(): Compute gene x species matrix from the result of Distatis

DistatisFast(): Fast implementation the multivariate analysis method Distatis

PreparePhylterData(): Prepare data for phylter analysis

carnivora: 125 genes trees for 53 carnivora species

detect.outliers() detect.outliers.array(): Detection of outliers in 1D and 2D data

impMean(): Imputation of missing values in a collection of matrices

medcouple(): A robust measure of skewness for univariate data

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

phylter(): Filter phylogenomics datasets

plot(<phylter>) plot2WR() plotDispersion() plotRV() plotopti(): Plot phylter objects

print(<phylter>): Print phylter objects

print(<phylterfinal>): print objects of class phylterfinal

print(<phylterinitial>): print objects of class phylterinitial

print(<summary.phylter>): print summary of phylter objects

rename.genes(): Name or rename a list of gene trees or matrices

simtrees(): Simplistic simulation of gene trees with outliers

summary(<phylter>): Get summary for phylter objects

trees2matrices(): Convert phylogenetic trees to distance matrices

write.phylter(): Write summary of phyter analysis to file(s)