streamfind.data

R package with supporting data and other assets for the R package streamfind.

Installation

With R (>= 4.2.0) configured and pak installed:

pak::pkg_install("odea-project/streamfind.data")

Data Overview

Demo data is organized under inst/extdata/data/ by technique.

Mass Spectrometry (mass_spec/)

Demo	Path	Description
Basic TOF	mass_spec/basic_tof/	TOF data in centroid mzML, centroid mzXML, and profile mzML formats spiked with chemical and internal standards. Includes suspect list (suspects.csv) and internal standards (internal_standards.csv).
Basic Orbitrap	mass_spec/basic_orbitrap/	Orbitrap MS1-only data in profile mzML and mzXML formats.
Wastewater	mass_spec/wastewater/	TOF data from a wastewater analysis project with blanks, influent, and ozonated secondary effluent samples in positive and negative polarity. Includes suspect list (suspects.csv) and internal standards (internal_standards.csv).
MRM	mass_spec/mrm/	Multiple Reaction Monitoring data: estrogens (negative polarity, ms_spiked_estrogens.csv), nitrosamines (positive polarity), and environmental chemical standards (positive polarity).

Raman Spectroscopy (raman/)

Raman spectra of Bevacizumab drug product and blank measurements in .asc format.

Access Functions

# Mass spectrometry files
get_mass_spec_files()                                  # All MS files
get_mass_spec_basic_tof_files()                        # Basic TOF
get_mass_spec_basic_orbitrap_files()                   # Basic Orbitrap
get_mass_spec_wastewater_files()                       # Wastewater project
get_mass_spec_mrm_files()                              # MRM (all)
get_mass_spec_mrm_environment_files()                  # MRM environment
get_mass_spec_mrm_estrogens_files()                    # MRM estrogens
get_mass_spec_mrm_nitrosamines_files()                 # MRM nitrosamines

# Raman files
get_raman_files()                                      # All Raman .asc files

# CSV chemical lists (return file paths)
get_mass_spec_wastewater_suspects_csv()                # Wastewater suspects
get_mass_spec_wastewater_internal_standards_csv()      # Wastewater IS
get_mass_spec_basic_tof_suspects_csv()                 # Basic TOF suspects
get_mass_spec_basic_tof_internal_standards_csv()       # Basic TOF IS
get_mass_spec_mrm_estrogens_csv()                      # MRM estrogens

Read a CSV with data.table::fread():

library(data.table)
suspects <- fread(get_mass_spec_wastewater_suspects_csv())