get_dist: calculate distance

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

calculate distance

Usage

get_dist(obj, ...)

## S3 method for class 'data.frame'
get_dist(
  obj,
  distmethod = "euclidean",
  taxa_are_rows = FALSE,
  sampleda = NULL,
  tree = NULL,
  method = "hellinger",
  ...
)

## S3 method for class 'phyloseq'
get_dist(obj, distmethod = "euclidean", method = "hellinger", ...)

Arguments

obj	phyloseq, phyloseq class or data.frame nrow sample * ncol feature.
...,	additional parameters.
distmethod	character, default is "euclidean", see also distanceMethodList
taxa_are_rows	logical, default is FALSE.
sampleda	data.frame, nrow sample * ncol factors.
tree	object, the phylo class, see also as.phylo.
method	character, default is hellinger, see alse decostand

Value

distance class contianed distmethod and originalD attr

See Also

distance

Examples

data(test_otu_data)
distclass <- get_dist(test_otu_data)
hcsample <- get_clust(distclass)

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.