# Bayesian Model Optimized Reference Correction Method for Assigned and Unassigned Protein NMR Spectra

## Documentation for package ‘BaMORC’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

AA57OLMatrix | Overlapping Matrix for 57 amino acid and secondary structure combinations.
AA57OLWeights | Overlapping weights for 57 amino acid and secondary structure combinations.
aaCodes1Letter19 | Single-letter amino acid naming convention.
aaCodes1Letter20 | Single-letter amino acid naming convention.
aaCodes3Letter1stCap | Three-letter amino acid naming convention with first letter capitalized.
aaCodes3LetterAllCap | Three-letter amino acid naming convention with all letters capitalized.
aaCodes3LetterAllCap.v | Three-letter amino acid naming convention with all letters capitalized.
aaFreq | Pre-defined amino acid frequency data.
AvgCov.t | Average covariance across three secondary structures for all amino acid typings (including oxidized cystine).
bamorc | Calculates the referencing correction value.
calculate_aa_prob | Calculates an amino acid typing probability.
calculate_chi_squared_stat | Calculates a chi squared statistic(s).
calculate_mse | Calculates mean squared error
calculate_rcf | Calculates the relative cumulative frequency for amino acid and secondary structure.
CAMuTable | Mean chemical shift values for alpha carbon .
CarbonCov.t | Covariance values of chemical shifts of alpha and beta carbons.
CASdTable | Standard deviation of chemical shift values for alpha carbon .
CBMuTable | Mean chemical shift values for beta carbon .
CBSdTable | Standard deviation of chemical shift values for beta carbon .
chemicalShifts | Pre-defined sample chemical shifts data.
cname | All the amino acids and secondary structures combinations for easy access.
ID | RefDB ID included in the BaMORC package.
inverseMatrices | inverseMatrices.
jpred_fetcher | Using JPred Mass-submission scheduler program to submit protein sequence and return secondary structure results.
read_db_file | 'read_db_file()' reads in data from existing database that included in the BaMORC package. This database was extracted from RefDB database.
read_nmrstar_file | Extracts data from BMRB STAR 3.0 file. 'read_nmrstar_file()' parses BMRB STAR 3.0 file. It will extract sequence information and chemical shifts for both alpha and beta carbons.
read_raw_file | Extracts data from a protein NMR experimental peak list. 'read_raw_file()' function reads in a user provided protein NMR experimental peak list. It currently supports file format in csv, txt with deliminator of comma, whitespace or semicolon. Note: please don't leave space between sequence and chemical shifts data, otherwise it will report error.
RefDB.StatCA | Statistics of chemical shifts values of alpha carbons from RefDB.
RefDB.StatCB | Statistics of chemical shifts values of beta carbons from RefDB.
RefDB_data | RefDB object
unassigned_bamorc | Calculates the referencing correction value for unassigned protein NMR peaklists. 'unassigned_bamorc()' will analyze unassigned protein NMR spectra, first groups the peaklist via SSC, then estimates the secondary structure via JPred, finally using BaMORC core function to calculate the reference correction value.