bamorc: Calculates the referencing correction value.

In MoseleyBioinformaticsLab/BaMORC: Bayesian Model Optimized Reference Correction Method for Assigned and Unassigned Protein NMR Spectra

Description

The core package function that calculates the carbon-13 reference correction using an input protein sequence with associated secondary structure information along with a table of alpha and beta carbon chemical shift pairs. The output of this function is the correction value that should be added to the input carbon chemical shifts.

Usage

bamorc(sequence, secondary_structure = NULL, chemical_shifts_input,
  from = -5, to = 5)

Arguments

sequence	string of sequence
secondary_structure	string of secondary structure (optional)
chemical_shifts_input	table of alpha and beta carbon chemical shift pairs in data.frame
from	the lower bound of the optimization search window
to	the upper bound of the optimization search window

Value

Carbon-13 reference correction value that should be applied (added) to the input carbon chemical shifts data.

Examples

sequence <- paste(RefDB_data$carbonDat[[1]]$AA,collapse = "")
secondary_structure <- paste(RefDB_data$carbonDat[[1]]$SS,collapse = "")
chemical_shifts_input <- RefDB_data$carbonDat[[1]][,c(4,5)]
from=-5
to=5

## Not run: bamorc(sequence, secondary_structure, chemical_shifts_input, from=-5, to=5)

# Expected output
# [1] 0.0142443


sequence <- paste(BaMORC::RefDB_data$carbonDat[[1]]$AA,collapse = "")
chemical_shifts_input <- BaMORC::RefDB_data$carbonDat[[1]][,c(4,5)]
from=-5
to=5


## Not run: bamorc(sequence=sequence, chemical_shifts_input=chemical_shifts_input, from=-5, to=5)
# Expected output
# [1] 0.009805279

MoseleyBioinformaticsLab/BaMORC documentation built on May 12, 2019, 10:07 a.m.