mrbin (version 1.9.5)

annotatemrbin: 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,
  binwidth = 0.01,
  binheight = 1,
  dimension = "1D",
  metaboliteIdentities = NULL,
  add = FALSE,
  hideChemicalShift = FALSE,
  includeAll = FALSE,
  maxMetabolites = NULL,
  batchSize = 50,
  tiers = c(1, 2, 4, 5),
  peakRatio = c(0.67, 0.4, 0),
  Rmodifier = NULL,
  confirmationRthreshold = c(0.89, 0.84, 0.82),
  peakRthreshold = NULL,
  showMissing = FALSE,
  exclude = NULL,
  expandRange = 0,
  expandRangeFactor = 15,
  verbose = TRUE
)

Value

An (invisible) mrbin object

Arguments

mrbinObject

An mrbin object or matrix of bin intensities. In case of a matrix, the row names can be in the format left border, right border ("1.22,1.21") or the center of the bin ("1.215"). In the latter case, the parameters binwidth (and binheight if required) should be chosen accordingly. For 2D data, this would be "1.22,1.21,35,36" or "1.215,35.5"

annotate

If FALSE, the mrbin object will not be changed.

binwidth

Full width of each bin. Will only be used if mrbinObject is a matrix

binheight

Full height of each bin. Will only be used if mrbinObject is a matrix and dimension is set to "2D"

dimension

Dimension of NMR data set, option are "1D" or "2D" (e.g. for HSQC data). Will only be used if mrbinObject is a matrix

metaboliteIdentities

A numeric 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 chemical shift might make better plots.

includeAll

Should all metabolites in the predefined list be used, even if they aren't in the ordered list for this sample matrix?

maxMetabolites

Maximum number of metabolites to be used. Default is NULL (all metabolites in the list will be used)

batchSize

Look for this number of top metabolites first, then move n the next batch of lower-abundance metabolites

tiers

Should all tiers (1 through 5) of identification be applied? .

peakRatio

A threshold for the minimum ratio of significant peaks to total peaks to confirm an annotation

Rmodifier

A number by which the confirmationRthreshold is multiplied. This can be used to lower R threshold when signal-to-noise levels are low, such as in 2D spectra. If set to NULL (default), this will use 1 for 1D spectra and 0.4 for 2D spectra

confirmationRthreshold

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

peakRthreshold

A threshold to define the r-value cutoff that bins within one peak need to show to the first identified bin of the peak to be considered. If NULL, this will use .8 for 1D and .2 for 2D

showMissing

Should metabolites missing from the peak database be shown

exclude

Exclude specific metbolites from annotation, e.g. "DSS" if TSP was used instead.

expandRange

Expand the search range by this value in ppm. This could be used for low-field spectra.

expandRangeFactor

The expandRange will be multiplied by this value for the second, indirect dimension, e.g 13C.

verbose

Should outputs be shown or suppressed?

Examples

resetEnv()#clean up previous data from the package environment 
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,
                   NMRvendor="mrbin",
                   example=TRUE,#only used for the package examples
                   NMRfolders=c(system.file("extdata/3.mr1",package="mrbin"),
                              system.file("extdata/2.mr1",package="mrbin"),
                              system.file("extdata/1.mr1",package="mrbin"))))
metaboliteIdentities=matrix(c(1.346,1.324,21,23,1,1,
                              3.052,3.043,30.5,33.5,1,1),
                   ncol=6,byrow=TRUE)
rownames(metaboliteIdentities)=c("Lactate","Creatinine")
colnames(metaboliteIdentities)=c("left","right","top","bottom","usePeak1D","usePeak2D")
results<-annotatemrbin(results,metaboliteIdentities=metaboliteIdentities)
results$metadata$annotations[150:160]
plotPCA(results,loadings=TRUE)