unassigned_bamorc: Calculates the referencing correction value for unassigned...

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

Description

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.

Usage

unassigned_bamorc(peakList_file_loc, sequence,
  secondary_structure = NULL, from = -5, to = 5,
  ssc = "moseleybioinformaticslab/ssc",
  para = "--plformat=sparky --stype=HNcoCACB --dims=H,N,CA/CB --rdims=H,N")

Arguments

peakList_file_loc	NMR HNCACB file location
sequence	sequence string of protein of interest
secondary_structure	string of secondary structure if available
from	the lower bound of the optimization
to	the upper bound of the optimization
ssc	location of ssc docker image
para	parameter input for ssc function (no need to change)

Value

Reference correction value.

Examples

sequence = "RPAFCLEPPYAGPGKARIIRYFYNAAAGAAQAFVYGGVRAKRNNFASAADALAACAAA"
peakList_file_loc = system.file("extdata", "bpti_HNcoCACB.txt", package = "BaMORC")
## Not run: unassigned_bamorc(peakList_file_loc, sequence, secondary_structure=NULL,
from=-5, to=5, ssc="moseleybioinformaticslab/ssc",
para="--plformat=sparky --stype=HNcoCACB --dims=H,N,CA/CB --rdims=H,N")
## End(Not run)
# Expected result should be around (due to randomness): 0.0007890328

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