hs_preprocess: Calculate the phenotypic heterogeneity indices for each cell

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

Description

Calculate the phenotypic heterogeneity indices for each cell

Usage

hs_preprocess(
  hs.x,
  smooth = FALSE,
  align = FALSE,
  align_ref = 1,
  align_tol = 5,
  align_wind = 1,
  path = NULL,
  pattern = ".spc",
  trim.range = c(400, 1800),
  niter = 10
)

Arguments

hs.x	Available hyperspec object
smooth	Smoothing TRUE/FALSE. Defaults to FALSE.
align	Align spectra TRUE/FALSE. Defaults to FALSE.
align_ref	Spectrum to use as reference for the alignment. Defaults to 1, the first spectrum.
align_tol	Tolerance value for alignment. Defaults to 5.
align_wind	Window for alignment. Defaults to 1.
path	Path contain spc files if no hyperSpec object is available
pattern	Pattern of spc files to import from path
trim.range	Wavenumber range to trim from raw spectra.
niter	Number of iterations.

Examples

# Load hyperSpec object
data("hs_example")

# Load hyperSpec object
hs.x.proc <- hs_preprocess(hs.x = hs_example, smooth = FALSE)

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