Crop chromatograms

Restricts chromatograms to a range of retention times and/or wavelengths by subsetting the existing grid.

Usage

crop_chroms(x, rt_range = NULL, lambda_range = NULL)

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.

rt_range

Numeric vector of length 2 giving the inclusive range of retention times to keep, in the time unit of the data. Either element may be NA for an open bound. Defaults to NULL, which keeps every time point.

lambda_range

Numeric vector of length 2 giving the inclusive range of wavelengths to keep. Either element may be NA for an open bound. Defaults to NULL, which keeps every wavelength.

Value

The cropped data, in the same shape as x.

Details

Cropping is pure subsetting: the returned data are a submatrix of the input, so values and dimnames pass through verbatim. This is the difference from cropping via preprocess, which reaches a narrower range by interpolating onto a new axis — resampling the signal unless the requested grid happens to coincide with the existing time points, and reformatting the retention times either way.

Bounds are inclusive, and either end of a range may be NA to leave it open. Ranges are expressed in the units of the data itself: retention times in whatever unit the chromatogram carries, as returned by get_times, and wavelengths as labeled in the column names, as returned by get_lambdas.

An "estimated_baseline" attribute attached by preprocess or correct_baseline is cropped alongside the data, so it stays aligned and can still be retrieved with get_baseline.

A range that does not overlap the data at all is an error. A range that merely extends past one end is honored as far as the data allow, with a warning reporting what was actually kept, since this is usually a typo or a unit mismatch. Cropping chromatograms whose time axes are offset from one another — as unaligned chromatograms generally are — can leave them with different numbers of rows, which also warns: functions that read the time axis from the first chromatogram would then mislabel the rest, so align before cropping if the result needs a common time axis.

See also

preprocess, correct_baseline, get_times, get_lambdas

Other preprocessing functions: correct_baseline(), preprocess(), subtract_blanks()

Author

Ethan Bass

Examples

data(Sa_pr)
cropped <- crop_chroms(Sa_pr, rt_range = c(12, 16))
trimmed <- crop_chroms(Sa_pr, lambda_range = c(220, NA))