Package 'mrbin'

Title: Metabolomics Data Analysis Functions
Description: A collection of functions for processing and analyzing metabolite data. The namesake function mrbin() converts 1D or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time. The function fia() ranks features according to their impact on classifier models, especially artificial neural network models.
Authors: Matthias Klein [aut, cre]
Maintainer: Matthias Klein <[email protected]>
License: GPL-3
Version: 1.9.0
Built: 2025-03-12 18:16:40 UTC
Source: https://github.com/kleinomicslab/mrbin

Help Index

A function for adding NMR spectra to the plot list.

Description

This function adds a spectrum to the plot list.

Usage

addToPlot(
  folder = NULL,
  dimension = "1D",
  NMRvendor = "Bruker",
  useAsNames = "Folder names",
  add = TRUE,
  omitCurrent = FALSE
)

Arguments

folder

Defines the exact NMR data folder. If NULL, mrbin parameter set is used
dimension

Defines the data dimension, "1D" or "2D". Only used if not NULL
NMRvendor

Defines the NMR manufacturer, default is "Bruker"
useAsNames

How should sample names be generated
add

Add spectra to existing list, or replace existing spectra. Default is TRUE
omitCurrent

Omit the "current spectrum" spot and start filling the additional lists immediately. Default is FALSE

Value

none

Examples

addToPlot()

A function for annotating mrbin objects.

Description

This function annotates an mrbin object and returns it with updated $annotations vector

Usage

annotatemrbin(
  mrbinObject,
  annotate = TRUE,
  metaboliteIdentities = NULL,
  add = FALSE,
  hideChemicalShift = FALSE,
  hideTentativeIds = FALSE,
  confirmationRthreshold = 0.6,
  confirmationPthreshold = 5e-06,
  checkBaselineCorrelation = TRUE
)

Arguments

mrbinObject

An mrbin object
annotate

If FALSE, the mrbin object will not be changed.
metaboliteIdentities

A numeric 4-column matrix or the file path for a .csv file containing such a matrix, the first columns containing metabolite names and the first row being a header. Each row belongs to one unique metabolite signal (left, right, top, bottom borders). Row names are metabolite names. If provided, this will overwrite any current metaboliteIdentities matrix present in the mrbin object. If missing, data currently attached to the mrbin object (if any) will be used.
add

Should the new metabolite list be added to an existing list, or replace the current list?
hideChemicalShift

Should the chemical shift (bin borders) of an identified metabolite be removed, leaving only the metabolite id, or should both be shown? Showing both helps in identifying signals of interest, but hiding the chmical shift might make better plots.
hideTentativeIds

Should the identities of tentative ids be omitted for clarity?
confirmationRthreshold

A threshold to define the r-value cutoff to confirm an annotation
confirmationPthreshold

A threshold to define the p-value cutoff to confirm an annotation
checkBaselineCorrelation

Should correlation to baseline be compared to confirm an annotation

Value

An (invisible) mrbin object

Examples

results<-mrbin(silent=TRUE,
                   parameters=list(verbose=TRUE,dimension="1D",PQNScaling="No",
                   binwidth1D=0.04,signal_to_noise1D=1,PCA="No",binRegion=c(9.5,0.5,10,156),
                   saveFiles="No",referenceScaling="No",noiseRemoval="No",
                   fixNegatives="No",logTrafo="No",noiseThreshold=.05,tryParallel=TRUE,
                   NMRfolders=c(system.file("extdata/3/10/pdata/10",package="mrbin"),
                              system.file("extdata/2/10/pdata/10",package="mrbin"),
                              system.file("extdata/1/10/pdata/10",package="mrbin"))))
metaboliteIdentities=matrix(c(1.346,1.324,21,23,
                              4.12,4.1,70.8578,71.653,
                              3.052,3.043,30.5,33.5,
                              4.066,4.059,57,59.5),
                   ncol=4,byrow=TRUE)
rownames(metaboliteIdentities)=c("Lactate","Lactate","Creatinine","Creatinine")
results<-annotatemrbin(results,metaboliteIdentities=metaboliteIdentities)
results$metadata$annotations[125:135]
plotPCA(results,loadings=TRUE)

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.

Usage

atnv(NMRdata, noiseLevels = NULL, verbose = TRUE, errorsAsWarnings = FALSE)

Arguments

NMRdata

A matrix or mrbin object containing NMR data. For matrix: columns=frequencies,rows=samples
noiseLevels

A vector (can be omitted if NMRdata is an mrbin object)
verbose

Should a summary be displayed if NMRdata is an mrbin object
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 NMR data without negative values.

Examples

resetEnv()
 results<-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(results$bins<=0)
 exampleNMRpositive<-atnv(NMRdata=results$bins, noiseLevels=results$parameters$noise_level_adjusted)
 sum(exampleNMRpositive<=0)

A function for checking mrbin objects.

Description

This function checks an mrbin object and returns warning if changes were not documented

Usage

checkmrbin(mrbinObject, verbose = TRUE, errorsAsWarnings = NULL)

Arguments

mrbinObject

An mrbin object
verbose

Should a summary be displayed? (Warnings will be displayed even when setting verbose to FALSE)
errorsAsWarnings

If TRUE, errors will be turned into warnings. Should be used with care, as errors indicate undocumented changes to the data. If not provided, this will be taken from the mrbinObject.

Value

An (invisible) character vector of warnings

Examples

mrbinObject<-createmrbin()
mrbinObject<-checkmrbin(mrbinObject)

A function for changing plotNMR plots.

Description

This function decreases the minimum contour level of the current 2D NMR spectrum plot.

Usage

contMin(refreshPlot = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE

Value

None

Examples

resetEnv()
mrbin(silent=TRUE,parameters=list(dimension="2D",binwidth2D=0.5,
         binheight=3,PQNScaling="No",referenceScaling="No",binRegion=c(4,3,60,65),
         noiseRemoval="No",trimZeros="No",cropHSQC="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,saveFiles="No",
         NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"))))
plotNMR()
contMin()

A function for changing plotNMR plots.

Description

This function increases the minimum contour level of the current 2D NMR spectrum plot.

Usage

contPlus(refreshPlot = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE

Value

None

Examples

resetEnv()
addToPlot(folder=system.file("extdata/1/12/pdata/10",package="mrbin"),dimension="2D")
plotNMR()
contPlus()

A function for creating mrbin objects.

Description

This function creates an mrbin object and returns it.

Usage

createmrbin()

Value

An (invisible) mrbin object

Examples

mrbinObject<-createmrbin()

A function for cropping HSQC spectra.

Description

This function crops HSQC spectra to the region along the diagonal to remove uninformative signals. Will work only for 1H-13C HSQC spectra.

Usage

cropNMR()

Value

None

Examples

resetEnv()
results<-mrbin(silent=TRUE,
         parameters=list(dimension="2D",binwidth2D=1,binheight=4,cropHSQC="No",PCA="No",
         PQNScaling="No",noiseRemoval="No",removeSolvent="No",verbose=TRUE,tryParallel=TRUE,
         NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"))))
cropNMR()

A function for scaling to individual dilution factors.

Description

This function performs sample-wise scaling of binned data to correct for dilution through different sample volumes used, or for different sample weights. All bin values of one sample are multiplied by the corresponding dilution factor.

Usage

dilutionCorrection(mrbinResults, verbose = TRUE, errorsAsWarnings = FALSE)

Arguments

mrbinResults

An mrbin object
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 mrbin object containing scaled NMR data.

Examples

results<-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"))),
         metadata=list(dilutionFactors=c(.75,1,.5)))
results<-dilutionCorrection(results)

A function for changing plotNMR plots.

Description

This function moves down the plot region of the current NMR plot (only 2D).

Usage

down(refreshPlot = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE

Value

None

Examples

resetEnv()
mrbin(silent=TRUE,parameters=list(dimension="2D",binwidth2D=0.5,
         binheight=3,PQNScaling="No",referenceScaling="No",binRegion=c(4,3,60,65),
         noiseRemoval="No",trimZeros="No",cropHSQC="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,saveFiles="No",
         NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"))))
plotNMR()
zoomIn()
down()

A function for editing metabolite identities.

Description

This function edits the metabolite list within an mrbin object and returns it

Usage

editmetabolitesmrbin(
  mrbinObject,
  borders = NULL,
  metabolitenames = NULL,
  add = FALSE,
  ids = NULL
)

Arguments

mrbinObject

An mrbin object
borders

A matrix of signal borders. 1D: two columns: left, right. 2D: four columns: left, right, top, bottom
metabolitenames

A character vector of metabolite identities
add

Should the new metabolite list be added to an existing list, or replace the current list?
ids

A matrix of potential metabolite identities. This has to be a 4-column matrix with columns indicating left, right, top, bottom. Rownames are metabolite names. If this matrix is not provided, borders and metabolitenames have to be provided.

Value

An (invisible) mrbin object

Examples

results<-mrbin(silent=TRUE,
                   parameters=list(verbose=TRUE,dimension="1D",PQNScaling="No",
                   binwidth1D=0.04,signal_to_noise1D=1,PCA="No",binRegion=c(9.5,0.5,10,156),
                   saveFiles="No",referenceScaling="No",noiseRemoval="No",
                   fixNegatives="No",logTrafo="No",noiseThreshold=.05,tryParallel=TRUE,
                   NMRfolders=c(system.file("extdata/2/10/pdata/10",package="mrbin"),
                              system.file("extdata/3/10/pdata/10",package="mrbin"))
                   ))
 results<-editmetabolitesmrbin(results,borders=matrix(c(
     1.346,1.324,
     4.12,4.1,
     3.052,3.043,
     4.066,4.059
   ),ncol=2,byrow=TRUE),metabolitenames=c(
   "Lactate",
   "Lactate",
   "Creatinine",
   "Creatinine"
   ))
results$parameters$metaboliteIdentities

A function for editing mrbin objects.

Description

This function edits an mrbin object and returns it. This is the only documented way to edit mrbin objects, all other ways of editing such object might cause warning message

Usage

editmrbin(
  mrbinObject,
  functionName = "mrbin::editmrbin",
  versionNumber = as.character(utils::packageVersion("mrbin")),
  bins = NULL,
  parameters = NULL,
  metadata = NULL,
  transformations = NULL,
  comment = "",
  verbose = TRUE
)

Arguments

mrbinObject

An mrbin object
functionName

Name of the package and function calling this command
versionNumber

Version number of the package calling this command
bins

A matrix containing values to be written to the mrbin object
parameters

A list containing values to be written to the mrbin object parameters, names must be names of the mrbin object, e.g. dimension
metadata

A list containing values to be written to the mrbin object parameters, names must be names of the mrbin object
transformations

An optional character vector describing any used data transformations or scaling such as reference scaling, PQN, log, atnv, etc.
comment

An optional character vector describing the change
verbose

Should a summary be displayed?

Value

An (invisible) mrbin object

Examples

mrbinObject<-createmrbin()
mrbinObject<-editmrbin(mrbinObject)

A function identifying features of importance.

Description

This function finds features that can change the outcomes of a model's prediction. Example: fia=1.00 means single compound found in all but 0 percent of samples. fia=2.45 indicates this compound is found in pairs in all but 45 percent of tested samples A function named predict needs to be present for this to work. If the function name of the prediction function is different, the function name has to be provided in the parameter functionNamePredict.

Usage

fia(
  model,
  dataSet,
  factors,
  nSeed = 6,
  numberOfSamples = 100,
  maxFeatures = 10000,
  innerLoop = 300,
  verbose = TRUE,
  maxNumberAllTests = 5,
  firstLevel = 1,
  saveMemory = FALSE,
  kerasClearMemory = 0,
  functionNamePredict = "predict",
  parameterNameObject = "object",
  parameterNameData = "x",
  ...
)

Arguments

model

A predictive model. Make sure to have loaded all required packages before starting this function
dataSet

An object containing data, columns=features, rows=samples. This should be either a matrix or a dataframe, depending on which of these two the specific prediction function requires
factors

A factor vector with group membership of each sample in the data set. Order of levels must correspond to the number predicted by the model
nSeed

Number of times that the test will be repeated, selecting different random features
numberOfSamples

Number of samples that will be randomly chosen from each group
maxFeatures

Maximum number of features that will be tested. Larger numbers will be split into child nodes without testing to increase speed
innerLoop

Number of repeated loops to test additional child nodes
verbose

A logical vector to turn messages on or off
maxNumberAllTests

Combinations of features of this length or shorter will not be split in half to create two children, but into multiple children with one feature left out each. This is done make sure no combination is missed.
firstLevel

Numeric value of first level or group. Usually 1 but for glm such as in the example this needs to be 0.
saveMemory

Save memory by performing only two predictions per step, which will be much slower. If you are using keras, use parameter kerasClearMemory=2 instead to free more memory and be a lot faster. FALSE to turn off.
kerasClearMemory

Save memory by clearing model from memory and reloading the model between chunks of predictions. Will only work when using package keras. 0=off, 1=medium (reload between repeat with different seeds), 2=maximum memory savings (reload after each run for a single sample). This will write a model file to the working directory.
functionNamePredict

The name of the prediction function. This only needs to be changed if the prediction function is not called predict
parameterNameObject

The name of the parameter for passing the model to the prediction function
parameterNameData

The name of the parameter for passing the data to the prediction function
...

Optional, additional parameters that will be passed to the prediction function.

Value

A list of results: scoresSummary A vector of fia scores for the whole dataset; scores contains vectors of fia scores for each predicted group; scoresIndividual A list of fia scores for each individual sample; fiaListPerSample A list of important combinations of features for each predicted sample; fiaMatrix A list of fia scores for each predicted group.

Examples

#First, define group membership and create the example feature data
 group<-factor(c(rep("Group1",4),rep("Group2",5)))
 names(group)<-paste("Sample",1:9,sep="")
 dataset<-data.frame(
   Feature1=c(5.1,5.0,6.0,2.9,4.8,4.6,4.9,3.8,5.1),
   Feature2=c(2.6,4.0,3.2,1.2,3.1,2.1,4.5,6.1,1.3),
   Feature3=c(3.1,6.1,5.8,5.1,3.8,6.1,3.4,4.0,4.4),
   Feature4=c(5.3,5.2,3.1,2.7,3.2,2.8,5.9,5.8,3.1),
   Feature5=c(3.2,4.4,4.8,4.9,6.0,3.6,6.1,3.9,3.5),
   Feature6=c(6.8,6.7,7.2,7.0,7.3,7.1,7.2,6.9,6.8)
   )
 rownames(dataset)<-names(group)
 #train a model - here we use a logit model instead of ANN as a demonstration
 mod<-glm(group~Feature1+Feature2+Feature3+Feature4+Feature5+Feature6,
   data=data.frame(group=group,dataset),family="binomial")
 fiaresults<-fia(model=mod,dataSet=dataset,factors=group,parameterNameData="newdata",
   firstLevel=0,type="response")
 fiaresults$scores

A function for saving the package environment.

Description

This function returns a list of all objects of the current package environment. This may be helpful for debugging or for accessing NMR spectral data and the raw bin data.

Usage

getEnv()

Value

A list containing all objects from the local package environment.

Examples

tempList<-getEnv()

A function for changing plotNMR plots.

Description

This function decreases the intensity of the current NMR spectrum plot.

Usage

intMin(dimension = "1D", refreshPlot = TRUE, value = NULL)

Arguments

dimension

Dimension to use. Defaults to "1D"
refreshPlot

Refresh plot automatically. Defaults to TRUE
value

Set exact value. Defaults to NULL

Value

None

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()
intMin()

A function for changing plotNMR plots.

Description

This function increases the intensity of the current NMR spectrum plot.

Usage

intPlus(dimension = "1D", refreshPlot = TRUE)

Arguments

dimension

Dimension to use. Defaults to "1D"
refreshPlot

Refresh plot automatically. Defaults to TRUE

Value

None

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()
intPlus()

A function for changing plotNMR plots.

Description

This function moves left the plot region of the current NMR plot.

Usage

left(refreshPlot = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE

Value

None

Examples

resetEnv()
mrbin(silent=TRUE,parameters=list(dimension="1D",binwidth1D=.5,
         noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         PQNScaling="No",saveFiles="No",referenceScaling="No",
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()
zoomIn()
left()

A function for log transforming data.

Description

This function performs logarithm transformation. Will not work with negative data.

Usage

logTrafo(mrbinResults, verbose = TRUE, errorsAsWarnings = FALSE)

Arguments

mrbinResults

An mrbin object
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 mrbin object

Examples

resetEnv()
results<-mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D", logTrafo="No",
                    binwidth1D=0.05,signal_to_noise1D=50,verbose=TRUE,PCA="No",tryParallel=TRUE,
                    NMRfolders=c(system.file("extdata/1/10/pdata/10",package="mrbin"),
                                system.file("extdata/2/10/pdata/10",package="mrbin"))))
results<-logTrafo(results)

A function for interactively editing metadata of mrbin objects.

Description

This function edits interactively or non-interactively the metadata filed of the provided mrbin object.

Usage

metadatamrbin(mrbinResults, metadata = NULL, graphics = graphics)

Arguments

mrbinResults

An mrbin object
metadata

An optional list of objects to be changed. If provided, interactive mode is deactivated
graphics

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

Value

An invisible mrbin object

Examples

results<-mrbin(silent=TRUE,
                   parameters=list(verbose=TRUE,dimension="1D",PQNScaling="No",
                   binwidth1D=0.04,signal_to_noise1D=1,PCA="No",binRegion=c(9.5,0.5,10,156),
                   saveFiles="No",referenceScaling="No",noiseRemoval="No",
                   fixNegatives="No",logTrafo="No",noiseThreshold=.05,tryParallel=TRUE,
                   NMRfolders=c(system.file("extdata/2/10/pdata/10",package="mrbin"),
                              system.file("extdata/3/10/pdata/10",package="mrbin"))
                   ))
 results<-metadatamrbin(results,metadata=list(projectTitle="Test project"))

A function setting the parameters and performing binning and data processing

Description

This function guides the user through the set-up of parameters, starts binning and performs the chosen data processing steps. If a list of parameters is provided and silent is set to TRUE, no user input is requested and binning and data processing are performed silently.

Usage

mrbin(
  silent = FALSE,
  setDefault = FALSE,
  parameters = NULL,
  metadata = NULL,
  graphics = TRUE
)

Arguments

silent

If TRUE, the user will be asked no questions and binning and data analysis will run according to the current parameters. Defaults to FALSE.
setDefault

If TRUE, all current parameters will be replaced by the default parameters (before loading any provided parameters sets). Defaults to FALSE.
parameters

Optional: A list of parameters, see examples for details. If omitted, the user will be asked through a series of question to set the parameters.
metadata

Optional: A list of metadata. If omitted, the user can add metadata after generating bin data.
graphics

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

Value

An invisible object of type "mrbin" containing bins (data after processing), parameters, and factors

Examples

# Set parameters in command line.
results<-mrbin(silent=TRUE,setDefault=TRUE,parameters=list(
                dimension="1D",binwidth1D=0.01,tryParallel=TRUE,
                signal_to_noise1D=25,noiseThreshold=0.75,useAsNames="Spectrum titles",
                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"))
                ))

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
)

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.

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,useAsNames="Spectrum titles",
   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"),
                system.file("extdata/3/12/pdata/10",package="mrbin"))))
results<-mrbinrun()

A function for plotting heatmaps.

Description

This function plots heatmaps based on rank order, using heatmap from the stats package

Usage

mrheatmap(
  results,
  binlist = NULL,
  samplelist = NULL,
  annotate = FALSE,
  cexRow = 0.7,
  cexCol = 0.8,
  margins = c(4, 6),
  Colv = NA,
  Rowv = NULL,
  closeDevice = TRUE,
  ...
)

Arguments

results

Either an mrbin object or a numeric matrix containing sample names as rownames and feature names as columns names.
binlist

A vector containing bin names as they are generated by mrbin (colnames). If provided, only these columns will be shown.
samplelist

A vector containing sample names (rownames). If provided, only these rows will be shown.
annotate

Should peak annotations be shown? This requires annotation data in the mrbin object.
cexRow

Font size for row labels
cexCol

Font size for column labels
margins

Determines the plot margins.
Colv

Determines if and how the column dendrogram should be computed and reordered. Default: NA (dendrogram will not be used)
Rowv

Determines if and how the row dendrogram should be computed and reordered. Default: NULL (dendrogram will be used)
closeDevice

Should previous plots be closed prior to plotting?
...

Additional graphical parameters that will be passed to the stats function heatmap

Value

None

Examples

resetEnv()
# First create NMR bin data, then plot some differential bins.
results<-mrbin(silent=TRUE,setDefault=TRUE,parameters=list(verbose=FALSE,
                dimension="1D",binwidth1D=0.01,PCA="No",showSpectrumPreview="No",
                signal_to_noise1D=25,noiseThreshold=0.75,useAsNames="Spectrum titles",
                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"))
                ))
metadata<-c(0,0,1)
#Find significant signals
pvalues<-rep(NA,ncol(results$bins))
names(pvalues)<-colnames(results$bins)
for(i in 1:ncol(results$bins)){
	model<-stats::lm(intensity~treatment, 
     data=data.frame(intensity=results$bins[,i],treatment=metadata))
	pvalues[i]<-stats::anova(model)$"Pr(>F)"[1]
}
significantBins<-names(sort(pvalues)[1:30]) 
metaboliteIdentities=matrix(c(1.346,1.324,21,23,
                              4.12,4.1,70.8578,71.653,
                              3.052,3.043,30.5,33.5,
                              4.066,4.059,57,59.5,
                              5.7,6.0,0,150),
                   ncol=4,byrow=TRUE)
#Annotate the dataset with signal identities
rownames(metaboliteIdentities)=c("Lactate","Lactate","Creatinine","Creatinine","Urea")
results<-annotatemrbin(results,metaboliteIdentities=metaboliteIdentities)
mrheatmap(results=results,
    binlist=significantBins,annotate=TRUE,
    main="Significant signals")

A function for plotting NMR spectra.

Description

This function plots NMR spectra. A menu of commands is displayed to edit the plot view and add spectra. Multiple spectra will be overlaid, and if both 1D and 2D spectra are selected, they are shown in two plots with matched ranges.

Usage

mrplot(
  hideMenu = FALSE,
  folders = NULL,
  dimensions = NULL,
  intensity1D = NULL,
  zoom = NULL,
  color = NULL,
  background = NULL,
  lwd = 1,
  plotTitle = "",
  showNames = "Spectrum titles",
  graphics = TRUE,
  highlight = NULL,
  binlist = NULL,
  annotate = NULL,
  metaboliteIdentities = NULL,
  ...
)

Arguments

hideMenu

Do not show the menu. Defaults to FALSE
folders

Optional vector of folder names of spectra to load. Defaults to NULL
dimensions

Optional vector dimensions of spectra to load. Defaults to NULL
intensity1D

Optional value of initial 1D intensity. Defaults to NULL
zoom

Optional vector of initial zoom area. Defaults to NULL
color

Defines the color of the spectrum plot. If NULL, a rainbow theme is used for 2D NMR
background

Background color, defaults to NULL (no background fill, usually results in a white background)
lwd

Line width, defaults to 1
plotTitle

Plot title, defaults to "" (empty)
showNames

Display list of spectrum titles in plot, defaults to "Spectrum titles". Other options are "" and "Folder names"
graphics

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

A vector of up to 2 frequencies that will be highlighted in the plot. If 2 values are provided the distance in Hz is shown as well. Defaults to NULL.
binlist

Optional: A vector containing bin names as they are generated by mrbin. These bins will be marked by rectangles in the plot. This could be useful for metabolite identification when having a list of significantly changing signals. Default is NULL.
annotate

Should peak annotation regions be shown?
metaboliteIdentities

Optional: A file path or 4-column matrix where each row belongs to one unique metabolite signal (left, right, top, bottom borders). Row names are metabolite names. For a file, this needs to be the file path for a .csv file containing such a matrix, the first columns containing metabolite names and the first row being a header. Each row belongs to one unique metabolite signal (left, right, top, bottom borders). Row names are metabolite names.
...

Additional graphical parameters that will be passed to the functions plot, lines, and/or contour

Value

None

Examples

resetEnv()
metaboliteIdentities=matrix(c(1.346,1.324,21,23,
                              4.12,4.1,70.8578,71.653,
                              3.052,3.043,30.5,33.5,
                              4.066,4.059,57,59.5,
                              2.582,2.479,46,49,
                              2.737,2.634,46,49),
                   ncol=4,byrow=TRUE)
rownames(metaboliteIdentities)=c("Lactate","Lactate","Creatinine","Creatinine","Citrate","Citrate")
mrplot(folders=c(system.file("extdata/1/12/pdata/10",package="mrbin"),
                 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")),
       dimensions=c("2D","1D","1D","1D"),zoom=c(2.8,2.4,20,60),
       highlight=c(2.564,2.537),
       binlist=c("2.725,2.675","2.575,2.525"),
       annotate=TRUE,metaboliteIdentities=metaboliteIdentities,
       plotTitle="Significant Bins",intensity1D=24,hideMenu=TRUE)

A function for plotting NMR spectra.

Description

This function plots the current NMR spectrum. If no parameters are provided, parameters are read from the mrbin.env environment variables, set by mrbin. To change the plot, use zoom(), zoomIn(), zoomOut(), intPlus(), intMin(), left(), right(). For 2D data use additionally: contMin(), contPlus(), up(), down()

Usage

plotMultiNMR(
  region = NULL,
  rectangleRegions = NULL,
  rectangleColors = c("darkseagreen3", "orange", "blue", "red", "yellow", "gray",
    "purple"),
  density = NULL,
  cex.axis = 0.7,
  rectangleFront = FALSE,
  correctOffset2D = TRUE,
  polygonRegion = NULL,
  maxPlots = Inf,
  setContours = TRUE,
  color = NULL,
  add = FALSE,
  showGrid = FALSE,
  buffer = TRUE,
  manualScale = TRUE,
  plotTitle = "",
  renewSpectrum = TRUE,
  restrictToRange = FALSE,
  enableSplit = TRUE,
  dimension = NULL,
  lwd = 1,
  background = NULL,
  titles = NULL,
  plotCurrent = TRUE,
  ...
)

Arguments

region

A vector defining the plot region (left, right, top, bottom) or "all" for the whole spectrum
rectangleRegions

A 4-column matrix defining areas where to plot rectangles
rectangleColors

Define colors for the rectangles
density

Shading lines for the rectangles
cex.axis

Font size of axis tick labels.
rectangleFront

Plot rectangles in front of spectrum rather than in background (only 2D)
correctOffset2D

Do a basic offset correction so 2D spectra have a baseline close to 0. Defaults to TRUE
polygonRegion

Defines 4 corners of a polygon to be plotted
maxPlots

The maximum number of 2D plots to be overlaid
setContours

Should upper and lower contour levels be calculated of the old ones be reused? Default: TRUE
color

Defines the color of the spectrum plot. If NULL, a rainbow theme is used for 2D NMR
add

If TRUE, additional spectrum plots are overlaid with the current plot
showGrid

Shows a grid of data points. Defaults to FALSE
buffer

Speed up plotting by loading a plot. Defaults to TRUE
manualScale

If TRUE, scaling factor is taken from environment variables
plotTitle

Defines the main title of the plot
renewSpectrum

Should a new size-reduced spectrum for quicker plotting be calculated, or can the old one be used? Default: TRUE
restrictToRange

Restrict plot area to range of available data points. Defaults to FALSE
enableSplit

Allow split plots for showing 1D and 2D spectra simultaneously
dimension

If not provided, this will be taken from package environment
lwd

Line width, defaults to 1
background

Background color, defaults to NULL (no background fill, usually results in a white background)
titles

Display list of spectrum titles in plot, defaults to NULL
plotCurrent

Should the first (current) spectrum in the list be plotted, defaults to TRUE
...

Additional graphical parameters that will be passed to the functions plot, lines, and/or contour

Value

None

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotMultiNMR()

A function for plotting NMR spectra.

Description

This function plots the current NMR spectrum. If no parameters are provided, parameters are read from the mrbin.env environment variables, set by mrbin. To change the plot, use zoom(), zoomIn(), zoomOut(), intPlus(), intMin(), left(), right(). For 2D data use additionally: contMin(), contPlus(), up(), down()

Usage

plotNMR(
  region = NULL,
  rectangleRegions = NULL,
  rectangleColors = c("darkseagreen3", "orange", "blue", "red", "yellow", "gray",
    "purple"),
  density = NULL,
  rectangleFront = FALSE,
  polygonRegion = NULL,
  color = NULL,
  add = FALSE,
  showGrid = FALSE,
  manualScale = TRUE,
  plotTitle = "",
  title = NULL,
  titleCounter = NULL,
  hideNegative = FALSE,
  restrictToRange = FALSE,
  currentSpectrumOriginal = NULL,
  spectrumTMP = NULL,
  renewSpectrum = TRUE,
  cex.axis = 0.7,
  perspective = FALSE,
  noise = NULL,
  dimension = NULL,
  plotDelay = 0.1,
  lwd = 1,
  background = NULL,
  ...
)

Arguments

region

A vector defining the plot region (left, right, top, bottom) or "all" for the whole spectrum
rectangleRegions

A 4-column matrix defining areas where to plot rectangles
rectangleColors

Define colors for the rectangles
density

Shading lines for the rectangles
rectangleFront

Plot rectangles in front of spectrum rather than in background (only 2D)
polygonRegion

Defines 4 corners of a polygon to be plotted
color

Defines the color of the spectrum plot. If NULL, a rainbow theme is used for 2D NMR
add

If TRUE, additional spectrum plots are overlaid with the current plot
showGrid

Shows a grid of data points. Defaults to FALSE
manualScale

If TRUE, scaling factor is taken from environment variables
plotTitle

Defines the main title of the plot
title

Display the spectrum title in plot, defaults to NULL
titleCounter

Count of the spectrum title for positioning in plot, defaults to NULL
hideNegative

Should negative parts of the 2D spectrum be hidden? Defaults to FALSE
restrictToRange

Restrict plot area to range of available data points. Defaults to FALSE
currentSpectrumOriginal

Optional spectral data. If omitted, data from the environment variables is used
spectrumTMP

A size-reduced spectrum for quicker plotting. Defaults to NULL
renewSpectrum

Should a new size-reduced spectrum for quicker plotting be calculated, or can the old one be used? Default: TRUE
cex.axis

Font size of axis tick labels.
perspective

If TRUE, a perspective plot will be displayed for 2D data instead of the regular topographic view
noise

If provided, a line or plane at this level will be added to the plot to indicate noise level
dimension

"1D' or "2D". If not provided, this will be deduced from the data
plotDelay

Add a small delay in seconds to force RStudio to update plots
lwd

Line width, defaults to 1
background

Background color, defaults to NULL (no background fill, usually results in a white background)
...

Additional graphical parameters that will be passed to the functions plot, lines, and/or contour

Value

An (invisible) dimension-reduced spectrum, either a matrix or a vector

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()

A function for plotting PCA plots.

Description

This function performs PCA, then plots PC1 and PC2.

Usage

plotPCA(
  mrbinResults,
  defineGroups = TRUE,
  loadings = FALSE,
  legendPosition = "bottomleft",
  annotate = TRUE,
  verbose = TRUE
)

Arguments

mrbinResults

An mrbin object
defineGroups

Should groups be colored differently?
loadings

Should loadings be plotted instead of scores?
legendPosition

Where should the legend be plotted, Defaults to "left", other options include "top", "topright", etc.
annotate

Should loadings be annotated with metabolite identities, if available in $metadata?
verbose

Should a summary be displayed?

Value

An invisible prcomp result object

Examples

results<-mrbin(silent=TRUE,setDefault=FALSE,parameters=list(dimension="2D",
    binRegion=c(8,1,15,140),binwidth2D=0.1,binheight=4,solventRegion=c(5.5,4.2),
    PQNScaling="No",noiseRemoval="Yes",trimZeros="Yes",tryParallel=TRUE,
    fixNegatives="No",logTrafo="No",PCA="No",signal_to_noise2D=10,
    NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"),
                 system.file("extdata/2/12/pdata/10",package="mrbin"),
                 system.file("extdata/3/12/pdata/10",package="mrbin"))))
plotPCA(results)

A function for plotting quality indicators, including PCA plots.

Description

This function plots boxplots (bin-wise and sample-wise) as visual quality indicators. It also performs PCA, then plots PC1 and PC2 and loading plots.

Usage

plotResults(mrbinResults, defineGroups = TRUE, process = TRUE, silent = FALSE)

Arguments

mrbinResults

An mrbin object
defineGroups

Should group membership be highlighted in PCA?
process

If set to FALSE, the file name will be extended by "Raw" to indicate that data has not been processed yet
silent

If set to TRUE, plots will be saved but not shown for the binning step for speed purposes

Value

None

Examples

results<-mrbin(silent=TRUE,setDefault=FALSE,parameters=list(dimension="2D",
    binRegion=c(8,1,15,140),binwidth2D=0.2,binheight=4,solventRegion=c(5.5,4.2),
    PQNScaling="No",noiseRemoval="Yes",trimZeros="Yes",tryParallel=TRUE,
    fixNegatives="No",logTrafo="No",PCA="No",signal_to_noise2D=10,
    NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"),
                 system.file("extdata/2/12/pdata/10",package="mrbin"))))
plotResults(results)

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

results<-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"))))
results<-PQNScaling(results)

A function returning predicted values for use with the fia function.

Description

This function predicts group membership and returns a numeric vector with results.

Usage

predictWrapper(
  model,
  dataSet,
  functionNamePredict = "predict",
  firstLevel = 1,
  parameterNameObject = "object",
  parameterNameData = "x",
  dataFrameFlag = FALSE,
  ...
)

Arguments

model

A predictive model. Make sure to have loaded all required packages before starting this function
dataSet

A matrix or dataframe containing data, depending on what your predict function requires. Columns=features, rows=samples
functionNamePredict

The name of the prediction function. This only needs to be changed if the prediction function is not called predict
firstLevel

Numeric value of first level or group. Usually 1 but for glm such as in the example this needs to be 0.
parameterNameObject

The name of the parameter for passing the model to the prediction function
parameterNameData

The name of the parameter for passing the data to the prediction function
dataFrameFlag

Logical value indicating whether the data object is a data frame rather than a matrix.
...

Optional, additional parameters that will be passed to the prediction function.

Value

A numeric (integer) vector of predicted group memberships.

Examples

#First, define group membership and create the example feature data
 group<-factor(c(rep("Group1",4),rep("Group2",5)))
 names(group)<-paste("Sample",1:9,sep="")
 dataset<-data.frame(
   Feature1=c(5.1,5.0,6.0,2.9,4.8,4.6,4.9,3.8,5.1),
   Feature2=c(2.6,4.0,3.2,1.2,3.1,2.1,4.5,6.1,1.3),
   Feature3=c(3.1,6.1,5.8,5.1,3.8,6.1,3.4,4.0,4.4),
   Feature4=c(5.3,5.2,3.1,2.7,3.2,2.8,5.9,5.8,3.1),
   Feature5=c(3.2,4.4,4.8,4.9,6.0,3.6,6.1,3.9,3.5)
   )
 rownames(dataset)<-names(group)
 #train a model - here we use a logit model instead of ANN as a demonstration
 mod<-glm(group~Feature1+Feature2+Feature3+Feature4+Feature5,
   data=data.frame(group=group,dataset),family="binomial")
 predictWrapper(model=mod,dataSet=dataset,firstLevel=0,type="response")

A function for printing parameters to the screen.

Description

This function reads parameters from the global variable mrbin.env$mrbin$parameters and prints the required R code for creating a data set to the screen.

Usage

printParameters()

Value

None

Examples

printParameters()

A function for changing and adding variables in the package environment.

Description

This function can change variables in the current package environment. This may be helpful for debugging or for some plotting functions.

Usage

putToEnv(variableList)

Arguments

variableList

A list containing all objects to be saved in the local package environment.

Value

None

Examples

putToEnv(list(bins=NULL))

A function for reading Bruker NMR spectra.

Description

This function reads Bruker NMR data. 1D and 2D data are supported.

Usage

readBruker(
  folder = NULL,
  dimension = NULL,
  onlyTitles = FALSE,
  useAsNames = "Spectrum titles",
  checkFiles = FALSE
)

Arguments

folder

Defines the exact NMR data folder. If NULL, mrbin parameter set is used
dimension

Defines the data dimension, "1D" or "2D". Only used if not NULL
onlyTitles

Read only spectrum titles, but no data. Defaults to FALSE
useAsNames

How should sample names be generated
checkFiles

Only check if the folder exists or contains NMR data. Defaults to FALSE

Value

An (invisible) list containing spectral data and the spectrum name

Examples

exampleData<-readBruker(folder=system.file("extdata/1/10/pdata/10",package="mrbin"),
                        dimension="1D")

A function recreating parameters from previous runs.

Description

This function reads parameters from a text file that was created during a previous run or mrbin(). After reading, the data can be recreated using mrbin(). File names in $parameters might need to be updated.

Usage

recreatemrbin(filename = NULL, graphics = TRUE)

Arguments

filename

File path/name of the mrbin parameter file to be loaded
graphics

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

Value

None

Examples

# Insert full folder path and file name
recreatemrbin(system.file("extdata/mrbin.txt",package="mrbin"))

A function for removing NMR spectra from the plot list.

Description

This function removes a spectrum from the plot list.

Usage

removeFromPlot(folder = NULL, dimension = "1D")

Arguments

folder

Defines the exact NMR data folder.
dimension

Defines the data dimension, "1D" or "2D".

Value

none

Examples

removeFromPlot()

A function for removing bins below noise level.

Description

This function checks for each bin (column) whether its level is below the individual noise level times the signal-to-noise ratio. If less than the defined threshold level are above noise*SNR, the whole bin is removed.

Usage

removeNoise(mrbinResults, verbose = TRUE, errorsAsWarnings = FALSE)

Arguments

mrbinResults

An mrbin object
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 mrbin object

Examples

results<-mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",
                    binwidth1D=0.05,noiseRemoval="No",PQNScaling="No",tryParallel=TRUE,
                    fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
                    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"))))
results<-removeNoise(results)

A function for removing a spectrum.

Description

This function lets the user pick spectra from a list for removal from data analysis.

Usage

removeSpectrum(
  mrbinResults = NULL,
  spectra = NULL,
  verbose = TRUE,
  errorsAsWarnings = FALSE,
  graphics = TRUE
)

Arguments

mrbinResults

An mrbin object. If not provided, the function works on the package environment
spectra

Character vector with NMR folder names to be excluded. If provided, no interactive selection will be shown
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.
graphics

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

Value

An invisible mrbin object (only if an mrbin object was provided)

Examples

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

A parameter resetting function

Description

This function resets the parameter variables.

Usage

resetEnv()

Value

None

Examples

resetEnv()

A function for changing plotNMR plots.

Description

This function moves right the plot region of the current NMR plot.

Usage

right(refreshPlot = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE

Value

None

Examples

resetEnv()
mrbin(silent=TRUE,parameters=list(dimension="1D",binwidth1D=.5,
         noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         PQNScaling="No",saveFiles="No",referenceScaling="No",
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()
zoomIn()
right()

A function for interactively setting the current spectrum.

Description

This function lets the user pick a spectrum from the list of spectra analysis. This function is meant only for use within the mrbin function.

Usage

setCurrentSpectrum(spectrumNumber = NULL, graphics = TRUE)

Arguments

spectrumNumber

If provided, this number will be used; defaults to NULL
graphics

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

Value

None

Examples

setCurrentSpectrum(spectrumNumber=1)

A function for setting dilution factors.

Description

This function edits the dilution factors of an mrbin object but does not change the bin data.

Usage

setDilutionFactors(
  mrbinObject,
  dilutionFactors = NULL,
  errorsAsWarnings = FALSE,
  alwaysShowOptionKeep = FALSE,
  graphics = TRUE
)

Arguments

mrbinObject

An mrbin object
dilutionFactors

An optional vector of dilution factors. If provided, no user input is requested
errorsAsWarnings

If TRUE, errors will be turned into warnings. Should be used with care, as errors indicate undocumented changes to the data.
alwaysShowOptionKeep

If TRUE, you will be asked to keep current values even if they do not match the current dataset.
graphics

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

Value

An invisible mrbin object

Examples

results<-mrbin(silent=TRUE,
                   parameters=list(verbose=TRUE,dimension="1D",PQNScaling="No",
                   binwidth1D=0.04,signal_to_noise1D=1,PCA="No",binRegion=c(9.5,0.5,10,156),
                   saveFiles="No",referenceScaling="No",noiseRemoval="No",
                   fixNegatives="No",logTrafo="No",noiseThreshold=.05,tryParallel=TRUE,
                   NMRfolders=c(system.file("extdata/2/10/pdata/10",package="mrbin"),
                              system.file("extdata/3/10/pdata/10",package="mrbin"))
                   ))
 results<-setDilutionFactors(results,dilutionFactors=c(1.5,2))

A function for setting and plotting noise levels.

Description

This function reads parameters from the global variable mrbin.env$mrbin$parameters and plots exemplary spectra and respective noise levels. Plots will be saved if saveFiles is set to "Yes".

Usage

setNoiseLevels(
  mrbinObject,
  plotOnly = FALSE,
  showSpectrumPreview = NULL,
  silent = FALSE,
  graphics = TRUE
)

Arguments

mrbinObject

An mrbin object
plotOnly

Should only noise plots be generated (TRUE), or should noise levels be adjusted interactively (FALSE)
showSpectrumPreview

Should plots be shown? If not provided, this value will be taken from the mrbin object parameters
silent

If set to TRUE, plots will not be shown but might still be saved
graphics

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

Value

An invisible mrbin object

Examples

results<-mrbin(silent=TRUE,
                   parameters=list(verbose=TRUE,dimension="1D",PQNScaling="No",
                   binwidth1D=0.04,signal_to_noise1D=1,PCA="No",binRegion=c(9.5,0.5,10,156),
                   saveFiles="No",referenceScaling="No",noiseRemoval="No",
                   fixNegatives="No",logTrafo="No",noiseThreshold=.05,tryParallel=TRUE,
                   NMRfolders=c(system.file("extdata/2/10/pdata/10",package="mrbin"),
                              system.file("extdata/3/10/pdata/10",package="mrbin"))
                   ))
 results<-setNoiseLevels(results,plotOnly=TRUE)

A function for changing plotNMR plots.

Description

This function moves up or down the 1D plot region of the current NMR plot.

Usage

setOffset(offsetValue = NULL)

Arguments

offsetValue

The new offset value. Defaults to NULL

Value

None

Examples

setOffset(0)

A function setting parameters and checking for consistency.

Description

This function set parameters and checks parameters for consistency.

Usage

setParam(parameters = NULL, metadata = NULL)

Arguments

parameters

List of parameters to be set
metadata

List of metadata to be set

Value

None

Examples

setParam(parameters=list(dimension="1D"))

A function for time stamping mrbin objects.

Description

This function adds time stamps to an mrbin object and returns it. Is used only within functions making changes to mrbin objects.

Usage

timeStampMrbin(
  mrbinObject,
  functionName = "InProgress...",
  versionNumber = "0",
  changeDetails = "InProgress...",
  steps = 0,
  comment = ""
)

Arguments

mrbinObject

An mrbin object
functionName

Name of the package and function calling this command
versionNumber

Version number of the package calling this command
changeDetails

Details of changes made to the mrbin object
steps

Indicates which step to perform: 0 (only pre-change), 1 (only post-change)
comment

An optional character vector describing the change

Value

An (invisible) mrbin object

Examples

mrbinObject<-createmrbin()
mrbinObject<-timeStampMrbin(mrbinObject)

A function for trimming zero-values bins.

Description

This function removes zero-values bins. These might be created during removal of solvent and additional areas, or at the edges of the spectrum.

Usage

trimZeros(mrbinResults)

Arguments

mrbinResults

An mrbin object

Value

An invisible mrbin object

Examples

results<-mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D", logTrafo="No",
                    binwidth1D=0.05,signal_to_noise1D=50, verbose=TRUE, PCA="No",
                      trimZeros="No",tryParallel=TRUE,
                    NMRfolders=c(system.file("extdata/1/10/pdata/10",package="mrbin"),
                                system.file("extdata/2/10/pdata/10",package="mrbin"))))
results<-trimZeros(results)

A function for scaling to unit variance.

Description

This function performs scaling of binned data to unit variance so that each bin has variance 1 and mean 0. This is rarely necessary, but might be advantageous, e.g. in artificial neural networks.

Usage

unitVarianceScaling(mrbinResults, verbose = TRUE, errorsAsWarnings = FALSE)

Arguments

mrbinResults

An mrbin object
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 mrbin object containing scaled NMR data.

Examples

results<-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"))))
results<-unitVarianceScaling(results)

A function for changing plotNMR plots.

Description

This function moves up the plot region of the current NMR plot (only 2D).

Usage

up(refreshPlot = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE

Value

None

Examples

resetEnv()
mrbin(silent=TRUE,parameters=list(dimension="2D",binwidth2D=0.5,
         binheight=3,PQNScaling="No",referenceScaling="No",binRegion=c(4,3,60,65),
         noiseRemoval="No",trimZeros="No",cropHSQC="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,saveFiles="No",
         NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"))))
plotNMR()
zoomIn()
up()

A function for changing plotNMR plots.

Description

This function changes the plot region of the current NMR plot. Can be called with no arguments: zoom(). In this case the user will be asked for manual input.

Usage

zoom(
  left = NULL,
  right = NULL,
  top = NULL,
  bottom = NULL,
  refreshPlot = TRUE,
  dimension = "2D"
)

Arguments

left

New left boundary
right

New right boundary
top

New top boundary
bottom

New bottom boundary
refreshPlot

Refresh plot automatically. Defaults to TRUE
dimension

Dimension of the data. Defaults to "2D"

Value

An invisible value indicating if a change occurred

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()
zoom(left=4.6,right=2,top=10,bottom=150)

A function for changing plotNMR plots.

Description

This function zooms into the plot region of the current NMR plot.

Usage

zoomIn(refreshPlot = TRUE, x = TRUE, y = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE
x

Change x axis? Defaults to TRUE
y

Change y axis? Defaults to TRUE

Value

None

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()
zoomIn()

A function for changing plotNMR plots.

Description

This function zooms out from the plot region of the current NMR plot.

Usage

zoomOut(refreshPlot = TRUE, x = TRUE, y = TRUE)

Arguments

refreshPlot

Refresh plot automatically. Defaults to TRUE
x

Change x axis? Defaults to TRUE
y

Change y axis? Defaults to TRUE

Value

None

Examples

mrbin(silent=TRUE,setDefault=TRUE,parameters=list(dimension="1D",binwidth1D=.1,
         PQNScaling="No",noiseRemoval="No",trimZeros="No",tryParallel=TRUE,
         fixNegatives="No",logTrafo="No",PCA="No",verbose=TRUE,
         NMRfolders=system.file("extdata/1/10/pdata/10",package="mrbin")))
plotNMR()
zoomIn()
zoomOut()