mrbin (version 1.4.2)

atnv: A function replacing negative values.

Description

This function replaces (column-wise) negative values by a small positive number. The number is calculated as an affine transformation to the range of the lowest positive number to 0,01*the lowest positive number (of this column). Ranks stay unchanged. Positive numbers are not altered. If sample-wise noise levels are available, the median noise level of samples with negative values is calculated and replaces the lowest positive number in case it is smaller. If no noise data is available, the 1 positive values in the data set is used as an estimate. It is recommended to us this function AFTER noise removal and other data clean-up methods, as it may alter (reduce) the noise level. If no NMR data and noise levels are provided as arguments, the function will use NMR data and noise levels from the global variables mrbin.env$bins and mrbin.env$mrbinTMP.

Usage

atnv(NMRdata = NULL, noiseLevels = NULL)

Arguments

NMRdata

A matrix containing NMR data. Columns=frequencies,rows=samples

noiseLevels

A vector

Value

NMRdata An invisible matrix containing NMR data without negative values.

Examples

# NOT RUN {
 Example<-mrbin(silent=TRUE,
                   parameters=list(verbose=TRUE,dimension="1D",PQNScaling="No",
                   binwidth1D=0.005,signal_to_noise1D=1,PCA="No",binRegion=c(9.5,7.5,10,156),
                   saveFiles="No",referenceScaling="No",noiseRemoval="No",
                   fixNegatives="No",logTrafo="No",noiseThreshold=.05,
                   NMRfolders=c(system.file("extdata/2/10/pdata/10",package="mrbin"),
                              system.file("extdata/3/10/pdata/10",package="mrbin"))
                   ))
 sum(Example$bins<=0)
 exampleNMRpositive<-atnv(NMRdata=Example$bins, noiseLevels=Example$parameters$noise_level)
 sum(exampleNMRpositive<=0)
# }