pTreatGPL: 2D-NMR Global Peak List pre-treatments

In ManonMartin/MBXUCL: R Routines for metabolomic data

Description

Elimination of negative intensities (=0), Elimination of the water zone, Normalization of the intensities (sum = 1)

Usage

pTreatGPL(Intensities, Coordinates, LowW, UpW)

Arguments

Intensities	A numeric matrix of intensities (from individual GPL object).
Coordinates	A numeric matrix of coordinates (C1, C2).
LowW	Number corresponding to the lower value of the water zone to suppress (4.63).
UpW	Number corresponding to the upper value of the water zone to suppress (5.1).

Value

A pre-treated matrix of intensities (with rows = spectra)

Author(s)

Baptiste Feraud

Examples

path <-  system.file('extdata', package = 'MBXUCL')
GPL = read.table(file.path(path, 'UrineGPL.csv'), sep=',',
 header=TRUE, row.names = 1, na.strings = '.' )

Int = GPL[,seq(3,dim(GPL)[2]- 1, 2)]
Coord = GPL[,c(1,2)]
IntT <- pTreatGPL(Int, Coord, 4.63, 5.1)
IntT[,1:2]

ManonMartin/MBXUCL documentation built on Nov. 26, 2021, 8:45 p.m.