mrbinrun: A function performing all data read and processing steps.

In mrbin: Metabolomics Data Analysis Functions

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()

mrbin documentation built on June 22, 2024, 9:39 a.m.