Adaptive processing of LC-MS data

Documentation for package ‘recetox.aplcms’ version 0.10.1

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.