PQNScaling: A function for PQN scaling.

In mrbin: Metabolomics Data Analysis Functions

A function for PQN scaling.

Description

This function performs PQN scaling. To further exclude unreliable noise, only the most intense signals are used. For 1H and 1H-13C HSQC spectra, most of the sugar regions can be excluded to avoid a dominating effect of the multiple glucose signals.

Usage

PQNScaling(
  NMRdata,
  ignoreGlucose = "Yes",
  dimension = "1D",
  ppmNames = "borders",
  sugarArea = c(5.4, 3.35, 72, 100),
  minimumFeatures = 40,
  showHist = FALSE,
  verbose = TRUE,
  errorsAsWarnings = FALSE
)

Arguments

NMRdata	A matrix containing NMR data or an mrbin object. Columns=frequencies,rows=samples
ignoreGlucose	A character value ("Yes" or "No")
dimension	A character value ("1D" or "2D")
ppmNames	A character value ("borders" or "mean")
sugarArea	A numeric vector defining the the borders of glucose area
minimumFeatures	A numeric value defining minimum feature number used
showHist	A logical value, default is FALSE
verbose	Should a summary be printed?
errorsAsWarnings	If TRUE, errors will be turned into warnings. Should be used with care, as errors indicate undocumented changes to the data.

Value

An invisible matrix or mrbin object containing scaled NMR data.

Examples

mrbinResults<-mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",
                    binwidth1D=0.05,PQNScaling="No",PCA="No",tryParallel=TRUE,logTrafo="No",
                    NMRfolders=c(system.file("extdata/1/10/pdata/10",package="mrbin"),
                                system.file("extdata/2/10/pdata/10",package="mrbin"),
                                system.file("extdata/3/10/pdata/10",package="mrbin"))))
mrbinResults<-PQNScaling(mrbinResults)

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