PerformPeakAnnotation: Perform peak annotation
In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

Description Usage Arguments Value Author(s) References See Also Examples

This function performs peak annotation on the xset object created using the PerformPeakPicking function.

1	PerformPeakAnnotation(mSet, annotaParam, ncore = 1, running.controller = NULL)

`mSet`	mSet object, usually generated by 'PerformPeakProfiling' here.
`annotaParam`	The object created using the SetAnnotationParam function, containing user's specified or default parameters for downstream raw MS data pre-processing.
`ncore`	annotation running core. Default is 1. Parallel running will be supported soon.
`running.controller`	The resuming pipeline running controller. Optional. Don't need to define by hand.

will return an mSet object wirh annotation finished

Zhiqiang Pang zhiqiang.pang@mail.mcgill.ca, Jasmine Chong jasmine.chong@mail.mcgill.ca, and Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)

Kuhl C, Tautenhahn R, Boettcher C, Larson TR, Neumann S (2012). "CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84, 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g.

ExecutePlan and PerformPeakProfiling for the whole pipeline.

data(mSet);
newPath <- dir(system.file("mzData", package = "mtbls2"),
               full.names = TRUE, recursive = TRUE)[c(10, 11, 12)]
mSet <- updateRawSpectraPath(mSet, newPath);
annParams <- SetAnnotationParam(polarity = 'positive',
                                mz_abs_add = 0.035);

## Perform peak annotation with newly deinfed annParams
# mSet <- PerformPeakAnnotation(mSet = mSet,
#                               annotaParam = annParams,
#                               ncore =1)