An R Package for Data Preparation and Molecular Formula Assignment

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Documentation for package ‘MFAssignR’ version 1.1.0

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AddCalculatedSummary AddCalculatedSummary function
bind_and_filter_data Binds and filters two data frames
calculate_variables Calculate variables based on mass values
combine_isotopes Combines isotopes This function combines isotopes based on experimental mass.
compare_bad_and_filter Compare and filter isotopic and bad data
CompFactorToInt Component factor to integer
CompFactorToInt2 Example Data, masslist CHNOS_ML_Ex is a list of 2121 negative ion masses and their corresponding relative abundances. It contains monoisotopic CHO, CHNO, and CHOS molecules and serves as an example of data Component factor to integer
CompIntToFactor Component integer to factor
CompIntToFactor2 Component integer to factor
compute_combinations Computes all possible combinations of series This function computes all possible combinations of series. The number of combinations is specified by user.
compute_pairs Compute pairs based on specified criteria and filtering
create_data_chunks Creates data chunks
create_pairs Create pairs based on mass difference criteria
EM Expected masses of components
EM2 Expected masses of components
Even Even integer
extract_mono_and_iso_pairs Extracts mono and iso pairs from a data frame
FilterAndMerge FilterAndMerge function
filtered_data_is_empty Return TRUE if any of the elements in the list has a length of 0, otherwise FALSE
filter_and_arrange_data Filters and arranges data based on abundance and mass
filter_pairs Filter pairs based on mass difference error
FindCoreFormulae2 Assigns all possible combinations of C, H, and O for a given MW
FindCoreFormulae2_Halo Assigns all possible combinations of C, H, and O for a given MW
HighMoles Maximum limit of moles (user limit)
HistNoise Estimates the noise level
IsoFiltR Identifies and separates likely isotopic masses from monoisotopic masses
KMDNoise Estimates the Signal to Noise cut
LowMoles Minimum limit of moles (user limit)
MaxMoles Maximum limit of moles (program limit)
merge_and_filter_abundances Merges and filters abundances for mono and iso pairs
merge_and_filter_pairs Merges and filters mono and iso pairs
MFAssign Assigns all possible MF to each row of input data frame with CHOFIT and formula extension
MFAssignCHO Assigns all possible CHO molecular formulae to each row of input data frame
MinMoles Minimum limit of moles (program limit)
NM Nominal masses of components
plot_spectrum Plot Spectrum Function
processKnown Process Known Compounds
processMassList Process Mass List
process_carbon_isotoping Process carbon isotoping data
process_sulfur Process sulfur data
Recal Generates a plot to visualize recalibrant series, recalibrates two mass lists, and produces a list of the chosen recalibrants.
RecalList Identifies canditate series for recalibration
SNplot Plot of Mass Spectrum with highlighted S/N cut
sulfur_check Check sulfur data
Valence Valence of component
ValidFormula Determine if molecular formula is valid