get_ROIs: get_ROIs

In YasinEl/mzRAPP: Benchmark Dataset Generation and Non-Targeted Data Pre-Processing Assessment

get_ROIs

Description

Takes a the output of get_mz_table and adds columns with information on regions of interest (ROI).

Usage

get_ROIs(
  files,
  Target.table,
  minCentroids = 4,
  AccurateMZtol = 5,
  PrecisionMZtol = 5,
  plan = "multiprocess"
)

Arguments

files	vector containing all mzML file paths
Target.table	output of function get_mz_table
minCentroids	minimum number of consecutive scans > 0 for a ROI to be picked up (eq. to minCentroids argument in xcms:::findmzROI function)
AccurateMZtol	mass accuracy (systematic error tolerance) in +/- ppm; this value is used to recognize detected ROIs as the expected mz values calculated in get_mz_table. If multiple ROIs fit the same benchmark peak they are combined.
PrecisionMZtol	mass precision (random error tolerance) in +/- ppm; this value is used as for setting the maximum spread of scans within one ROI (equ. to "dev" argument * 1e-6 in xcms:::findmzROI)
plan	see plan

Details

eic_mzmin: lowest mz value detected in respective ROI

eic_mzmax: highest mz value detected in respective ROI

Value

data.table object with information on ROIs for each row in Target.table. additional columns from Target.table are retained

YasinEl/mzRAPP documentation built on Feb. 18, 2024, 11:49 a.m.