RawMS: Storing the raw mass spec data and operating on it

In MoseleyBioinformaticsLab/FTMS.peakCharacterization: Functionality for Detecting and Characterizing Peaks

Storing the raw mass spec data and operating on it

Description

This reference class represents a storage container for the raw mass-spec data from a zipped mzML file and associated metadata. It provides methods for plotting the total-ion chromatogram, and setting which scans will be used for peak picking

Usage

RawMS

Arguments

raw_file	the zip or mzML file to use
metadata_file	the metadata file to use

Format

An object of class R6ClassGenerator of length 25.

Details

The find_peaks() method is not set by default, it must be set by the user after instantiation. The find_peaks() function definition should take the raw_data, and either scan_range or rt_range. It should also store the function name that is actually used for finding the peaks, and the variables, and then generate a peaks object. See the examples below for how to generate these functions.

Value

A reference class with methods set_scans(), plot_tic(), find_peaks().

Examples

## Not run: 
# setting different files
rms <- raw_ms("mzmlFile.mzML")
rms <- raw_ms("mzmlFile.mzML", "someDirectoryForZip")

rms <- raw_ms("mzmlZipFile.zip")

# Plot the total-ion-chromatogram
rms$plot_tic()

rms$set_scans(scan_range = c(1, 2, 3))
rms$set_scans(rt_range = c(0, 50.1)) # uses seconds

# set the find_peaks method
rms$find_peaks <- function(){

}


## End(Not run)

MoseleyBioinformaticsLab/FTMS.peakCharacterization documentation built on April 27, 2022, 3:32 a.m.