apply.sonar.calibration: generate.sonar.calibration

In cbroeckl/calibrate.sonar: Functions for calibrating the quadrupole isolation range for waters sonar acquisition.

generate.sonar.calibration

Description

Create calibration parameters from a low collision energy SONAR scan - traditional or 'hybrid' Sonar

Usage

apply.sonar.calibration(
  raw.file = "C:/Users/cbroeckl/Documents/temp/hybridSonar.raw",
  sonar.cal = my.cal,
  recursive = FALSE
)

Arguments

raw.file	full path (or path within working directory) to the .RAW file to which the calibration is to be applied An entire directory can be input instead, and if a directory is chosen all appropriate .raw files in that directory will be calibrated.
sonar.cal	either an R object generated by 'generate.sonar.calibration, or a path to a csv calibration file written by generate.sonar.calibration.
recursive	logical. if 'raw.file' is a path to a directory of raw files, should the function also look for raw files in all subdirectories? see ?list.files

Details

This function uses Apex3D64.exe, distributed by Waters Corp, to perform 4d peak detection in SONAR data, reads that output data, filters, if desired, and calibrates the linear relationships between sonar drift bin and m/z value. An R-object is returned, and a .csv file exported. These data contain details on the instrumentation and acquisition method used to collect the calibration data, to ensure that the calibration is only applied to compatible data files. Masslynx Version, Instrument Serial number, and sonar settings must all match.

Value

returns nothing to the R environment

selected .RAW files will have been modified with a new _sonar.INF and optionally some file copying and renaming if using hybrid sonar.

Author(s)

Corey Broeckling

cbroeckl/calibrate.sonar documentation built on Sept. 18, 2023, 4:37 a.m.