mrbin (version 1.9.4)

mrbinrun: 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,
  graphics = TRUE
)

Value

An invisible mrbin object

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

graphics

Controls whether pop-up windows are shown for selections. Defaults to TRUE.

Examples

resetEnv()#clean up previous data from the package environment 
setParam(parameters=list(dimension="2D",binwidth2D=0.1,binheight=5,
   binRegion=c(8,1,15,140),PQNScaling="No",useAsNames="Spectrum titles",
   fixNegatives="No",logTrafo="No",signal_to_noise2D=10,solventRegion=c(5.5,4.2),
   example=TRUE,#only used for the package examples
   NMRfolders=c(system.file("extdata/1.mr2",package="mrbin"),
                system.file("extdata/2.mr2",package="mrbin"),
                system.file("extdata/3.mr2",package="mrbin")),
   NMRvendor="mrbin"))
results<-mrbinrun()