tsLib-class: Class for representing a reference library
In acinostroza/TargetSearch: A package for the analysis of GC-MS metabolite profiling data

tsLib-class

R Documentation

Class for representing a reference library

Description

This is a class representation of a reference GC library.

Details

Objects of this class are normally created by the function ImportLibrary, which is the recommended method, though they can be created manually as shown in the examples.

Use one of the methods described below to set or get the information of various slots. Most of them are self-evident, but we describe some methods in the following paragraphs.

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.

The c method requires that the combination of all objects have unique identifiers (names), or in other words, the objects cannot share identifiers. Duplicated identifiers are not allowed and an error will be thrown. Since TargetSearch 2.8.0, different column names of the libData slot (see method libData) are allowed, as long as the data types are characters, numeric, or logical. More complex type may or not may work.

Use the libUID method to set or get the library unique identifiers (also referred as libID). This is a short string used for internal object data checking. It is sometimes useful if these identifiers refer to identifiers of external databases, for example, KEGG identifiers. These identifiers are normally supplied via the libID column in the function ImportLibrary.

Note that the method libId is deprecated and may be removed in a future version of TargetSearch. Use the equivalent makeIndex instead. This method has nothing to do with unique identifiers like libUID.

Slots

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.

Methods

[: 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"): Deprecated. Use makeIndex instead.
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.
libUID: signature(obj = "tsLib"): gets the library unique identifiers, also know as libID.
libUID<-: signature(obj = "tsLib"): sets the library unique identifiers, also know as libID.
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.
c: Combine two or more tsLib objects.

Note

Accessing the object slots directly via the @ operator is not supported, in particular, using it to set slot values, because it could result in invalid objects. Always use the accessor methods to retrieve the information.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

Examples

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 selection 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)

# get and change the library identifiers
(gcID <- libUID(refLibrary))
libUID(refLibrary) <- c('GC_1', 'GC_2', 'GC_3')

#####################################################################
# objects can be subset and combined with the `[` and `c` operators
lib1 <- refLibrary[1:2]
lib2 <- refLibrary[3]
lib  <- c(lib1, lib2) # this restores the object refLibrary

#####################################################################
# These examples show how changing a quantitative or selective mass
# could lead to unexpected results.

# show quantMasses
quantMass(refLibrary)

# suppose 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 explicitly, noting that
# the first masses coincides with 96 (the quantMass)
selMass(refLibrary)[[1]] <- c(96, 204, 361)
topMass(refLibrary)[[1]] <- c(96, 204, 361)

acinostroza/TargetSearch documentation built on July 5, 2025, 1:19 a.m.