get_dist: calculate distance

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

calculate distance

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

## Not run: 
data(test_otu_data)
test_otu_data %<>% as.phyloseq()
distclass <- get_dist(test_otu_data)
hcsample <- get_clust(distclass)

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.