OmicFlow (version 1.5.0)

bray: Compute Bray-Curtis Dissimilarity from a Dense or Sparse Matrix.

Description

Calculates the Bray-Curtis dissimilarity of a Matrix pairwise for each column.

Usage

bray(x, weighted = TRUE, threads = 1)

Value

A column x column dist object.

Arguments

x

A matrix, sparseMatrix or Matrix.

weighted

A boolean value, to use abundances (weighted = TRUE) or absence/presence (weighted=FALSE) (default: TRUE).

threads

A wholenumber, the number of threads to use in setThreadOptions (default: 1).

Details

The Bray-Curtis dissimilarity between two samples \(A\) and \(B\), each of length \(n\), is defined as:

\(d(A,B) = \frac{\sum_{i}^n |A_i - B_i|}{\sum_{i}^n (A_i + B_i)}\)

where \(A_i\) and \(B_i\) are the abundances of the \(i\)-th feature in sample \(A\) and \(B\), respectively. When weighted is set to FALSE, counts are replaced by presence/absence data.

References

Bray, J.R. & Curtis, J.T. (1957) An Ordination of the Upland Forest Communities of Southern Wisconsin. Ecological Monographs, 27(4), 325–349.

Examples

library("OmicFlow")

metadata_file <- system.file("extdata", "metadata.tsv", package = "OmicFlow")
counts_file <- system.file("extdata", "counts.tsv", package = "OmicFlow")
features_file <- system.file("extdata", "features.tsv", package = "OmicFlow")
tree_file <- system.file("extdata", "tree.newick", package = "OmicFlow")

taxa <- metagenomics$new(
    metaData = metadata_file,
    countData = counts_file,
    featureData = features_file,
    treeData = tree_file
)

taxa$feature_subset(Kingdom == "Bacteria")
taxa$normalize()

bray(taxa$countData)