PerformDataTrimming: Perform raw MS data trimming

In xia-lab/MetaboAnalystR3.0: An R Package for Comprehensive Analysis of Metabolomics 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

PerformDataTrimming(
  datapath,
  mode = "ssm",
  write = F,
  mz,
  mzdiff,
  rt,
  rtdiff,
  rt.idx = 1/15,
  plot = T
)

Arguments

datapath	Character, the path of the raw MS data files' folder/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 trimed data to the directory 'trimed' 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.
plot	Logical, if ture, will plot the chromatogram of the trimed data.

Author(s)

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

xia-lab/MetaboAnalystR3.0 documentation built on May 6, 2020, 11:03 p.m.