PerformPeakAnnotation: Perform peak annotation

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

View source: R/Perform_functions.R

Description

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

Usage

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

Arguments

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.

Value

will return an mSet object wirh annotation finished

Author(s)

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)

References

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.

See Also

ExecutePlan and PerformPeakProfiling for the whole pipeline.

Examples

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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)

xia-lab/OptiLCMS documentation built on Sept. 6, 2021, 12:36 a.m.