Spectral data binning

Equidistant binning of spectra by summarising intensities within ppm bins.

Usage

binning(X, ppm = NULL, width = NULL, npoints = NULL, fun = sum)

Arguments

X

Numeric matrix or data frame with spectra in rows, or a named list as returned by read1d/read1d_proc containing X and ppm.

ppm

Numeric vector of chemical shift positions (length must match ncol(X)). If NULL, ppm is inferred in the following order:

1. X$ppm if X is a list input,

2. attr(X, "m8_axis")$ppm (if present),

3. numeric colnames(X) (if present).

width

Numeric. Bin size in ppm, or NULL if npoints is specified.

npoints

Integer. Desired number of bins per spectrum, or NULL if width is specified. If both are provided, npoints is used.

fun

Function. Summary function applied to intensities within each bin. Must return a single numeric value (e.g. sum, mean, max).

Value

Numeric matrix with spectra in rows and binned ppm variables in columns.

Details

If present, preprocessing provenance is appended to attr(X, "m8_prep") using .m8_stamp(). The ppm axis is updated in attr(X, "m8_axis")$ppm and column names are set to the bin centres.

When width is specified, spectra are interpolated onto a regular ppm grid and then aggregated within bins (interp = TRUE in provenance). When npoints is specified, aggregation is performed by index bins on the original grid (interp = FALSE in provenance).

See also

Other preprocessing: align_segment(), align_spectra(), calibrate(), correct_baseline(), correct_lw(), pqn(), print_preprocessing()

Examples

set.seed(1)
X <- matrix(rnorm(2 * 100), nrow = 2)
ppm <- round(seq(10, 0.5, length.out = 100), 3)
colnames(X) <- ppm

Xb <- binning(X, ppm, width = 0.5)
Xb_mean <- binning(X, ppm, width = 0.5, fun = mean)
dim(Xb)
#> [1]  2 19