mrbinrun {mrbin} | R Documentation |
A function performing all data read and processing steps.
Description
This function reads parameters from the global variable mrbin.env$mrbin$parameters and performs the following operations: Reading NMR files, creating bins, removing solvent area, removing additional user-defined areas, summing up bins that contain unstable peaks such as citric acid, removes noise bins, crops HSQC spectra to the diagonal area, performs PQN scaling, replaces negative values, log transforms and displays a PCA plot. Parameters are then saved in a text file. These can be recreated using recreatemrbin().
Usage
mrbinrun(createbins = TRUE, process = TRUE, mrbinResults = NULL, silent = TRUE)
Arguments
createbins |
If TRUE, new bin data is generated |
process |
If TRUE, bin data is processed, e.g. by noise removal, atnv, etc. |
mrbinResults |
An mrbin object. Needs to be provided only if createbins is FALSE |
silent |
If set to FALSE, no new time calculation is performed |
Value
An invisible mrbin object
Examples
resetEnv()
setParam(parameters=list(dimension="2D",binwidth2D=0.1,binheight=5,
binRegion=c(8,1,15,140),PQNScaling="No",tryParallel=TRUE,
fixNegatives="No",logTrafo="No",signal_to_noise2D=10,solventRegion=c(5.5,4.2),
NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"),
system.file("extdata/2/12/pdata/10",package="mrbin"))))
mrbinrun()