As explained in the Chromatograms class documentation, the Chromatograms
object is a container for chromatogram data that includes chromatographic
peaks data (retention time and related intensity values, also referred to
as peaks data variables in the context of Chromatograms) and metadata of
individual chromatograms (so called chromatograms variables).
The chromatograms variables information can be accessed using the
chromData() function. it is also possible to access specific
chromatograms variables using $.
chromData can be accessed, replaced but also filtered/subsetted. Refer to
the sections below for more details.
# S4 method for class 'Chromatograms'
chromData(object, columns = chromVariables(object), drop = FALSE)
# S4 method for class 'Chromatograms'
chromData(object) <- value
# S4 method for class 'Chromatograms'
chromVariables(object)
# S4 method for class 'Chromatograms'
chromIndex(object)
# S4 method for class 'Chromatograms'
chromIndex(object) <- value
# S4 method for class 'Chromatograms'
collisionEnergy(object)
# S4 method for class 'Chromatograms'
collisionEnergy(object) <- value
# S4 method for class 'Chromatograms'
dataOrigin(object)
# S4 method for class 'Chromatograms'
dataOrigin(object) <- value
# S4 method for class 'Chromatograms'
dataStorage(object)
# S4 method for class 'Chromatograms'
dataStorage(object) <- value
# S4 method for class 'Chromatograms'
msLevel(object)
# S4 method for class 'Chromatograms'
msLevel(object) <- value
# S4 method for class 'Chromatograms'
mz(object)
# S4 method for class 'Chromatograms'
mz(object) <- value
# S4 method for class 'Chromatograms'
mzMax(object)
# S4 method for class 'Chromatograms'
mzMax(object) <- value
# S4 method for class 'Chromatograms'
mzMin(object)
# S4 method for class 'Chromatograms'
mzMin(object) <- value
# S4 method for class 'Chromatograms'
length(x)
# S4 method for class 'Chromatograms'
precursorMz(object)
# S4 method for class 'Chromatograms'
precursorMz(object) <- value
# S4 method for class 'Chromatograms'
precursorMzMin(object)
# S4 method for class 'Chromatograms'
precursorMzMin(object) <- value
# S4 method for class 'Chromatograms'
precursorMzMax(object)
# S4 method for class 'Chromatograms'
precursorMzMax(object) <- value
# S4 method for class 'Chromatograms'
productMz(object)
# S4 method for class 'Chromatograms'
productMz(object) <- value
# S4 method for class 'Chromatograms'
productMzMin(object)
# S4 method for class 'Chromatograms'
productMzMin(object) <- value
# S4 method for class 'Chromatograms'
productMzMax(object)
# S4 method for class 'Chromatograms'
productMzMax(object) <- value
# S4 method for class 'Chromatograms'
filterChromData(
object,
variables = character(),
ranges = numeric(),
match = c("any", "all"),
keep = TRUE
)A Chromatograms object.
A character vector of chromatograms variables to extract.
A logical indicating whether to drop dimensions when extracting
a single variable.
replacement value for <- methods. See individual
method description or expected data type.
A Chromatograms object.
For filterChromData(): character vector with the names
of the chromatogram variables to filter for. The list of available
chromatogram variables can be obtained with chromVariables().
For filterChromData() : a numeric
vector of paired values (upper and lower boundary) that define the
ranges to filter the object. These paired values need to be in the
same order as the variables parameter (see below).
For filterChromData() : character(1)
defining whether the condition has to match for all provided
ranges (match = "all"; the default), or for any of them
(match = "any") for chromatogram data to be retained.
For filterChromData(): logical(1)
defining whether to keep (keep = TRUE) or remove (keep = FALSE)
the chromatogram data that match the condition.
The following chromatograms variables are guaranteed to be provided by a
Chromatograms object and to be accessible with either the chromData() or
a specific function named after the variables names:
chromIndex: an integer with the index of the chromatogram in the
original source file (e.g. mzML file).
collisionEnergy: for SRM data, numeric with the collision energy of
the precursor.
dataOrigin: optional character with the origin of a chromatogram.
dataStorage: character defining where the data is (currently) stored.
msLevel: integer defining the MS level of the data.
mz: optional numeric with the (target) m/z value for the
chromatographic data.
mzMin: optional numeric with the lower m/z value of the m/z range in
case the data (e.g. an extracted ion chromatogram EIC) was extracted from
a Spectra object.
mzMax: optional numeric with the upper m/z value of the m/z range.
precursorMz: for SRM data, numeric with the target m/z of the
precursor (parent).
precursorMzMin: for SRM data, optional numeric with the lower m/z of
the precursor's isolation window.
precursorMzMax: for SRM data, optional numeric with the upper m/z of
the precursor's isolation window.
productMz for SRM data, numeric with the target m/z of the
product ion.
productMzMin: for SRM data, optional numeric with the lower m/z of
the product's isolation window.
productMzMax: for SRM data, optional numeric with the upper m/z of
the product's isolation window.
Functions that filter Chromatograms based on chromatograms variables
(i.e, chromData ) will remove chromatographic data that do not meet the
specified conditions. This means that if a chromatogram is filtered out, its
corresponding chromData and peaksData will be removed from the object
immediately.
The available functions to filter chromatogram data are:
filterChromData(): Filters numerical chromatographic data variables
based on the provided numerical ranges. The method returns a
Chromatograms object containing only the chromatograms that match the
specified conditions. This function results in an object with fewer
chromatograms than the original.
Chromatograms for a general description of the Chromatograms
object.