chromatographR (version 0.4.4)

preprocess: Preprocess time/wavelength data

Description

Standard pre-processing of response matrices, consisting of a time axis and a spectral axis (e.g. HPLC-DAD/UV data). For smooth data, like UV-VIS data, the size of the matrix can be reduced by interpolation. By default, the data are baseline-corrected in the time direction (baseline.corr) and smoothed in the spectral dimension using cubic smoothing splines (smooth.spline.

Usage

preprocess(
  X,
  dim1,
  dim2,
  remove.time.baseline = TRUE,
  spec.smooth = TRUE,
  maxI,
  parallel,
  interpolate_rows = TRUE,
  interpolate_cols = TRUE,
  mc.cores = 2,
  ...
)

Value

The function returns the preprocessed data matrix, with row names and column names indicating the time points and wavelengths, respectively.

Arguments

X

A numerical data matrix, or list of data matrices. Missing values are not allowed. If rownames or colnames attributes are used, they should be numerical and signify time points and wavelengths, respectively.

dim1

A new, usually shorter, set of time points (numerical). The range of these should not be outside the range of the original time points, otherwise the function stops with an error message.

dim2

A new, usually shorter, set of wavelengths (numerical). The range of these should not be outside the range of the original wavelengths, otherwise the function stops with an error message.

remove.time.baseline

Logical, indicating whether baseline correction should be done in the time direction, according to baseline.corr. Default is TRUE.

spec.smooth

Logical, indicating whether smoothing should be done in the spectral direction, according to smooth.spline. Default is TRUE.

maxI

if given, the maximum intensity in the matrix is set to this value.

parallel

Logical, indicating whether to use parallel processing. Defaults to TRUE (unless you're on Windows).

interpolate_rows

Logical. Whether to interpolate along dim1. Defaults to TRUE.

interpolate_cols

Logical. Whether to interpolate along dim2. Defaults to TRUE.

mc.cores

How many cores to use for parallel processing. Defaults to 2.

...

Further optional arguments to baseline.corr.

Author

Ethan Bass

References

• Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. Fast parametric time warping of peak lists. Bioinformatics 31:3063-3065. tools:::Rd_expr_doi("10.1093/bioinformatics/btv299").

• Wehrens, R., Carvalho, E., Fraser, P.D. 2015. Metabolite profiling in LC–DAD using multivariate curve resolution: the alsace package for R. Metabolomics 11:1:143-154. tools:::Rd_expr_doi("10.1007/s11306-014-0683-5").

Examples

if (FALSE) { # interactive()
data(Sa)
new.ts <- seq(10,18.66,by=.01) # choose time-points
new.lambdas <- seq(200, 318, by = 2) # choose wavelengths
Sa_pr <- preprocess(Sa[[1]], dim1 = new.ts, dim2 = new.lambdas)
}