MassHunter_id_Summary: MassHunter report file (.cefs) parsing and summary

In MASHUOA/MassOmics: Data extraction pipeline for large-scale GC-MS metabolomics datasets

MassHunter report file (.cefs) parsing and summary

Description

This is a function to process the AMDIS_report.txt file. specify a in-house library or a subset of NIST library to find the most intense quantification ion within the GC-MS experiment m/z range. The script will invoke selection windows to let the user specify the files location.

Usage

MassHunter_id_Summary(
  workdir = NULL,
  MS.L = NULL,
  MassHunter.report = NULL,
  File.name = "Summary Report.csv",
  MsLibrary = c("NIST", "InHouse"),
  Ret.Time.Filter = 2.5,
  RT.shift.limt = 60,
  mz_L = 38,
  mz_U = 550,
  generate_rt_shift_graph = F,
  generate_rt_shift_graphs = F,
  RTcorrection = F
)

Arguments

workdir	locate the working Dir
MS.L	specify the library file
MsLibrary	specify the library file origin, could be "NIST" or "InHouse"
Ret.Time.Filter	set the retetion time filter window around the expected retention time (in +/-min).
RT.shift.limt	set a threshole in seconds to define a molecule have
mz_L	lower mz limit for quantification ion selection
mz_U	upper mz limit for quantification ion selection
generate_rt_shift_graph	Set TRUE to generate the retetion time shift plots for each molecules that have retention time discrepencies greater than the "RT.shift.limt"
RTcorrection	Set TRUE to enable a retention time correction before multiple peaks resolving
amdis.report	specify the identification report file

Value

None

Examples

MassHunter_id_Summary()

MASHUOA/MassOmics documentation built on Nov. 3, 2023, 10:48 p.m.