PerformROIExtraction: Perform ROI Extraction from raw MS data

In xia-lab/OptiLCMS: Optimized LC-MS Spectra Processing

Perform ROI Extraction from raw MS data

Description

This function performs the raw data trimming. This function will output an trimmed MSnExp file to memory or hardisk according to the choice of users must provide the data path for 'datapath', and optionally provide other corresponding parameters.

Usage

PerformROIExtraction(
  datapath,
  mode = "ssm",
  write = FALSE,
  mz,
  mzdiff,
  rt,
  rtdiff,
  rt.idx = 1/15,
  rmConts = TRUE,
  plot = TRUE,
  running.controller = NULL
)

Arguments

datapath	Character, the path of the raw MS data files' or folder's path (.mzXML, .CDF and .mzML) for parameters training.
mode	Character, mode for data trimming to select the chraracteristic peaks. Default is 'ssm'. Users could select random trimed according to mz value (mz_random) or RT value (rt_random). Besides, specific peaks at certain mz (mz_specific) or RT (rt_specific) could also be extracted. 'none' will not trim the data.
write	Logical, if true, will write the trimmed data to the directory 'trimmed' folder in the datapath. The data in memory will be kept.
mz	Numeric, mz value(s) for specific selection. Positive values means including (the values indicted) and negative value means excluding/removing.
mzdiff	Numeric, the deviation (ppm) of mz value(s).
rt	Numeric, rt value for specific selection. Positive values means including and negative value means excluding.
rtdiff	Numeric, the deviation (seconds) of rt value(s).
rt.idx	Numeric, the relative rt (retention time) range, from 0 to 1. 1 means all retention time will be retained, while 0 means none. Default is 1/15. If default rt.idx produce too few peaks, please consider increasing this value.
rmConts	LOgical, whether to exclude/remove the potential contamination for parameters optimization. Default is TRUE.
plot	Logical, if TRUE, will plot the chromatogram of the trimmed data.
running.controller	The resuming pipeline running controller. Optional. Don't need to define by hand.

Value

will return an mSet objects with extracted ROI

Author(s)

Zhiqiang Pang [e-mail] Jeff Xia [e-mail] Mcgill University License: GNU GPL (>= 2)

See Also

PerformDataTrimming for the old version of this function.

Examples

DataFiles <- dir(system.file("mzData", package = "mtbls2"), full.names = TRUE, recursive = TRUE)
# mSet <- PerformROIExtraction(datapath = DataFiles[1],rt.idx = 0.025, rmConts = FALSE);

xia-lab/OptiLCMS documentation built on Nov. 26, 2024, 3:50 a.m.