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

In microbiomeExplorer: Microbiome Exploration App

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")

microbiomeExplorer documentation built on Nov. 8, 2020, 8:16 p.m.