tsLib-class {TargetSearch} | R Documentation |
This is a class representation of a reference library.
Objects can be created by the function ImportLibrary
.
Name
:"character"
, the metabolite or analyte names.
RI
:"numeric"
, the expected retention time indices (RI) of the metabolites/analytes.
medRI
:"numeric"
, the median RI calculated from the samples.
RIdev
:"matrix"
, the RI deviation windows, k = 1,2,3. A three column matrix
selMass
:"list"
, every component is a numeric vector containing the selective masses.
topMass
:"list"
, every component is a numeric vector containing the top masses.
quantMass
:"numeric"
, the mass used for quantification.
libData
:"data.frame"
, additional library information.
spectra
:"list"
, the metabolite spectra. Each component is a two column matrix: m/z and intensity.
[
signature(x = "tsLib")
: Selects a subset of metabolites from the library.
$name
signature(x = "tsLib")
: Access column name
of libData
slot.
libId
signature(obj = "tsLib")
: Returns a vector of indices.
length
signature(x = "tsLib")
: returns the length of the library. i.e., number of metabolites.
libData
signature(obj = "tsLib")
: gets/sets the libData
slot.
libName
signature(obj = "tsLib")
: gets the Name
slot.
libRI
signature(obj = "tsLib")
: gets the RI
slot.
medRI
signature(obj = "tsLib")
: gets the medRI
slot.
refLib
signature(obj = "tsLib")
: Low level method to create a matrix representation of the library.
RIdev
signature(obj = "tsLib")
: gets the RI deviations.
RIdev<-
signature(obj = "tsLib")
: sets the RI deviations.
quantMass
signature(obj = "tsLib")
: gets the quantification mass.
quantMass<-
signature(obj = "tsLib")
: sets the quantification mass.
selMass
signature(obj = "tsLib")
: gets the selective masses.
show
signature(object = "tsLib")
: show method.
spectra
signature(obj = "tsLib")
: gets the spectra.
topMass
signature(obj = "tsLib")
: gets the top masses.
Some care is needed when using the methods quantMass<-
, selMass<-
, topMass<-
.
In order to be consistent, the first m/z value of the slot topMass
and selMass
are
equal to quantMass
, and the values of selMass
are equal to the first couple of values
of topMass
. In other words, the following constrain is applied.
quantMass : x[0] selMass : x[0], x[1], ..., x[k] topMass : x[0], x[1], ..., x[k], x[k+1], ..., x[n]
where 1 <= k <= n
and x[i]
is a m/z value. Thus, using one these methods will
change the values of the other slots. In the future, these methods will be deprecated, so it
is better to not rely on them.
See the last example on how this can lead to unexpected results.
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
showClass("tsLib") # define some metabolite names libNames <- c("Metab1", "Metab2", "Metab3") # the expected retention index RI <- c(100,200,300) # selective masses to search for. A list of vectors. selMasses <- list(c(95,204,361), c(87,116,190), c(158,201,219)) # define the retention time windows to look for the given selective masses. RIdev <- matrix(rep(c(10,5,2), length(libNames)), ncol = 3, byrow = TRUE) # Set the mass spectra. A list object of two-column matrices, or set to # NULL if the spectra is not available spectra <- NULL # some extra information about the library libData <- data.frame(Name = libNames, Lib_RI = RI) # create a reference library object refLibrary <- new("tsLib", Name = libNames, RI = RI, medRI = RI, RIdev = RIdev, selMass = selMasses, topMass = selMasses, spectra = spectra, libData = libData) # get the metabolite names libName(refLibrary) # set new names libName(refLibrary) <- c("Metab01", "Metab02", "Metab03") # get the expected retention times libRI(refLibrary) # set the retention time index for metabolite 3 to 310 seconds libRI(refLibrary)[3] <- 310 # change the seleccion and top masses of metabolite 3 selMass(refLibrary)[[3]] <- c(158,201,219,220,323) topMass(refLibrary)[[3]] <- c(158,201,219,220,323) # change the retention time deviations RIdev(refLibrary)[3,] <- c(8,4,1) ##################################################################### ##################################################################### # These examples show how changing a quantitaive or selective mass # could lead to unexpected results. # show quantMasses quantMass(refLibrary) # suposse that we want to change the quant mass of metabolite 1 to 96 due # to a typo in the library. We could do just quantMass(refLibrary)[1] <- 96 # however, we still see the mass 95 in the selective and top masses. selMass(refLibrary)[[1]] topMass(refLibrary)[[1]] # to remove the mass 95, set the topMass and selMass explicitely, noting that # the first masses coincides with 96 (the quantMass) selMass(refLibrary)[[1]] <- c(96, 204, 361) topMass(refLibrary)[[1]] <- c(96, 204, 361)