computeDistMat {microbiomeExplorer} | R Documentation

## 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")

[Package microbiomeExplorer version 1.4.0 Index]