PerformPeakProfiling: Perform peak profiling
In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

PerformPeakProfiling

R Documentation

Perform peak profiling

Description

This function performs feature extraction of user's raw MS data using the rawData object created using the ImportRawMSData function.

Usage

PerformPeakProfiling(
  mSet,
  Params = NULL,
  plotSettings,
  ncore,
  running.controller = NULL
)

Arguments

`mSet`	The object created using the ImportRawMSData function, containing the raw MS data.
`Params`	The object created using the SetPeakParam function, containing user's specified or default parameters for downstream raw MS data pre-processing.
`plotSettings`	List, plotting parameters produced by SetPlotParam Function. Defaut is set to true.
`ncore`	Numeric, used to define the cores' number for Peak Profiling.
`running.controller`	The resuming pipeline running controller. Optional. Don't need to define by hand.

Value

will return a complete mSet object with the whole processes 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)

Examples

##' Get raw spectra files
DataFiles <- dir(system.file("mzData", package = "mtbls2"), full.names = TRUE,
                 recursive = TRUE)[c(10:12, 14:16)]
##' Create a phenodata data.frame
pd <- data.frame(sample_name = sub(basename(DataFiles), pattern = ".mzData",
                                   replacement = "", fixed = TRUE),
                 sample_group = c(rep("col0", 3), rep("cyp79", 3)),
                 stringsAsFactors = FALSE)
##' Import raw spectra
mSet <- ImportRawMSData(path = DataFiles, metadata = pd);

##' Perform spectra profiling
mSet <- PerformPeakProfiling(mSet, Params = SetPeakParam(ppm = 15, 
                                                         bw = 10, 
                                                         mzdiff = 0.001, 
                                                         max_peakwidth = 15, 
                                                         min_peakwidth = 10), 
                                                         ncore = 2, 
                             plotSettings = SetPlotParam(Plot = TRUE))

##' Set peak annotation parameters
annParams <- SetAnnotationParam(polarity = 'positive',
                                mz_abs_add = 0.035);

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

##' Format the PeakList
mSet <- FormatPeakList(mSet = mSet,
                       annParams,
                       filtIso =FALSE,
                       filtAdducts = FALSE,
                       missPercent = 1)

##' Export the annotation result
Export.Annotation(mSet, path = tempdir());

##' Export the Peak Table
Export.PeakTable(mSet, path = tempdir());

##' Export the Peak summary
Export.PeakSummary(mSet, path = tempdir())

xia-lab/OptiLCMS documentation built on Nov. 6, 2024, 11:01 a.m.