cscs: Calculate CSCS distance

In askerdb/rCSCS: Compute the CSCS metric between metabolome samples

Description

Calculate CSCS distance

Usage

cscs(features, css, dissimilarity = T, cosine_threshold = 0.6,
  weighted = T, normalize = T)

Arguments

features	Matrix of feature intensities in each sample (pxn)
css	Square matrix of cosine similarities of features (pxp)
dissimilarity	Output dissimilarity matrix
cosine_threshold	Only include features below this threshold
weighted	Weight features by intensity (TRUE) or absence/presence (FALSE)

Details

The value of cosine_threshold is 0.6 in Sedio et al. but for certain applications other values might be better.

Value

A pxp matrix of CSCS distances

References

Sedio et al, 2016

Examples

#Get arbitrary GNPS project
gnps <- prepare_GNPS("0310e20491314ddbbf12d56b592548b4")
dist <- cscs(gnps$features, gnps$css)

#GlobalEuphorbia data
cscs(GEfeatures, GEcss)

askerdb/rCSCS documentation built on April 7, 2020, 10:51 a.m.