PerformParamsOptimization: Perform Parameters Optimization
In Zhiqiang-PANG/OptiLCMS_web: Optimized LC-MS Spectra Processing

Description Usage Arguments Author(s) Examples

This function is used to optimize the critical parameters of peak picking and alignment for the following data processing. It utilizes the trimed data and the internal instrument-specific parameters. Parallel computing will be performed. The number of cores user want to use could be specified.

PerformParamsOptimization(
  mSet,
  param = NULL,
  method = "DoE",
  ncore = 4,
  running.controller = NULL
)

`mSet`	mSet object, usually generated by 'PerformROIExtraction' or 'PerformDataTrimming' here.
`param`	List, Parameters defined by 'SetPeakParam' function.
`method`	Character, method of parameters optimization, including "DoE' only. Default is "DoE". Other method is under development.
`ncore`	Numeric, CPU threads number used to perform the parallel based optimization. If thers is memory issue, please reduce the 'ncore' used here. For default, 2/3 CPU threads of total will be used.
`running.controller`	The resuming pipeline running controller. Optional. Don't need to define by hand.

Zhiqiang Pang zhiqiang.pang@mail.mcgill.ca Jeff Xia jeff.xia@mcgill.ca Mcgill University License: GNU GPL (>= 2)

library(OptiLCMS)

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)

# mSet <- PerformROIExtraction(datapath = DataFiles[c(1:2)],rt.idx = 0.025,rmConts = FALSE);

# best_params <- PerformParamsOptimization(mSet, param = SetPeakParam(),ncore = 1);