# Adaptive processing of LC-MS data

## Documentation for package ‘recetox.aplcms’ version 0.10.1

- DESCRIPTION file.

## Help Pages

recetox.aplcms-package | Adaptive processing of LC/MS data
adaptive.bin | Adaptive binning
adjust.time | Adjust retention time across spectra.
combine.seq.3 | An internal function.
compute_clusters | Compute clusters of mz and rt and assign cluster id to individual features.
find.match | Internal function: finding the best match between a set of detected features and a set of known features.
find.tol | An internal function that is not supposed to be directly accessed by the user. Find m/z tolerance level.
find.tol.time | An internal function that find elution time tolerance level.
find.turn.point | Find peaks and valleys of a curve.
hybrid | Runs features extraction in hybrid mode.
interpol.area | Interpolate missing intensities and calculate the area for a single EIC.
load.lcms | Loading LC/MS data.
merge_features_and_known_table | A wrapper function to join knowledge from aligned features and known table.
proc.cdf | Filter noise and detect peaks from LC/MS data in CDF format
prof.to.features | Generate feature table from noise-removed LC/MS profile.
recetox.aplcms | Adaptive processing of LC/MS data
recover.weaker | Recover weak signals in some profiles that is not identified as a peak, but corresponds to identified peaks in other spectra.
rm.ridge | Removing long ridges at the same m/z.
run_filter | Continuity index.
semi.sup | Semi-supervised feature detection
two.step.hybrid | Two step hybrid feature detection.
unsupervised | Runs features extraction in unsupervised mode.