computeDistMat: Function to compute the distance matrix using vegdist from...

In zoecastillo/microbiomeExplorer: Microbiome Exploration App

Function to compute the distance matrix using vegdist from the vegan package

Description

Function to compute the distance matrix using vegdist from the vegan package

Usage

computeDistMat(aggdat, dist_method, log = TRUE, nfeatures = nrow(aggmat))

Arguments

aggdat	aggregated MRExperiment
dist_method	distance method from vegan package (See ?vegan::vegdist for details)
log	transform count matrix to log2; default is TRUE
nfeatures	number of features to use; default is all

Value

distance as dist

Examples

data("mouseData", package = "metagenomeSeq")
aggdat <- aggFeatures(mouseData, level = "genus")
computeDistMat(aggdat, dist_method = "bray")

zoecastillo/microbiomeExplorer documentation built on Sept. 11, 2022, 7:40 a.m.