An R Package for Data Preparation and Molecular Formula Assignment

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Documentation for package ‘MFAssignR’ version 1.0.3

• DESCRIPTION file.

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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_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
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