hs_type: Perform clustering of spectra using partitioning around...

In CMET-UGent/MicroRaman: Phenotyping of microbial Raman spectroscopy data

Description

Number of clusters is optimized based on Silhouette index.

Usage

hs_type(hs.x, PCA.var = NULL, ...)

Arguments

hs.x	hyperSpec object
PCA.var	Variance threshold for PCA preprocessing prior to clustering. Defaults to NULL which means that no PCA will be performed.
...	Parameters to pass on to pam().

Examples

## Short example

# Load hyperSpec object
data("hs_example")

# Convert to MassSpectrum object
hs.x.proc <- hs_preprocess(hs_example)

hclust_obj <- hs_type(hs.x.proc, PCA.var = 0.8)

CMET-UGent/MicroRaman documentation built on July 25, 2020, 6:20 p.m.