Preprocess time/wavelength data — preprocess • chromatographR

Standard preprocessing of time × wavelength response matrices (e.g. HPLC-DAD/UV data), consisting of: (i) baseline correction along the time axis, (ii) smoothing along the spectral axis, and (iii) optional interpolation in either dimension for dimensionality reduction. For densely sampled data, (e.g., UV-VIS spectra, the size of the matrix can be reduced by interpolation. By default, the data are baseline-corrected along the time axis using baseline.corr, and smoothed along the spectral axis using cubic smoothing splines (smooth.spline).

Usage

preprocess(
  X,
  dim1,
  dim2,
  remove.time.baseline = TRUE,
  spec.smooth = TRUE,
  maxI = NULL,
  interpolate_rows = TRUE,
  interpolate_cols = TRUE,
  cl = 2,
  show_progress = NULL,
  outlier_cutoff = 5/60,
  ...
)

Arguments

X: A numeric matrix (time × wavelength) or a list of such matrices. Row names must correspond to time points and column names to wavelengths.
dim1: Numeric vector specifying the target time grid. The data will be interpolated onto these time points. The range of the new values should not exceed the range of the original time points.
dim2: Numeric vector specifying the target wavelength grid. The data will be interpolated onto these wavelengths. The range of the new values should not exceed the range of the original wavelengths.
remove.time.baseline: Logical, indicating whether baseline correction should be done along the time axis, according to baseline.corr. Defaults to TRUE.
spec.smooth: Logical, indicating whether smoothing should be done along the spectral axis, according to smooth.spline. Defaults to TRUE.
maxI: If supplied, all values are rescaled so that the maximum intensity equals maxI.
interpolate_rows: Logical. Whether to interpolate along the time axis (dim1). Defaults to TRUE.
interpolate_cols: Logical. Whether to interpolate along the spectral axis (dim2). Defaults to TRUE.
cl: Either an integer specifying the number of cores to use for parallel processing or a cluster object created by makeCluster. Defaults to 2. On Windows integer values will be ignored.
show_progress: Logical. Whether to show progress bar. Defaults to TRUE if pbapply is installed.
outlier_cutoff: Threshold (in seconds) for excluding chromatograms that end earlier than expected. Samples ending more than this value before the median end time are removed. Defaults to 5 seconds. Only applies when dim1 is not specified.
...: Additional arguments to baseline.corr.

Value

The function returns the preprocessed data matrix (or list of matrices), with row names and column names indicating the time points and wavelengths, respectively.

Note

Adapted from the preprocess function in the alsace package by Ron Wehrens: https://github.com/rwehrens/alsace/blob/master/R/preprocess.R.

References

Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. Fast parametric time warping of peak lists. Bioinformatics 31:3063-3065. 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. doi:10.1007/s11306-014-0683-5 .

Author

Ethan Bass

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)
}