TargetSearch (version 1.28.1)

tsLib-class: Class for representing a reference library

Description

This is a class representation of a reference library.

Objects from the Class

Objects can be created by the function ImportLibrary.

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"): 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.

See Also

ImportLibrary

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 
# an empty list if the spectra is not available
spectra    <- list()
# 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)