chromData | R Documentation |
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 signature 'Chromatograms'
chromData(object, columns = chromVariables(object), drop = FALSE)
## S4 replacement method for signature 'Chromatograms'
chromData(object) <- value
## S4 method for signature 'Chromatograms'
chromVariables(object)
## S4 method for signature 'Chromatograms'
chromIndex(object)
## S4 replacement method for signature 'Chromatograms'
chromIndex(object) <- value
## S4 method for signature 'Chromatograms'
collisionEnergy(object)
## S4 replacement method for signature 'Chromatograms'
collisionEnergy(object) <- value
## S4 method for signature 'Chromatograms'
dataOrigin(object)
## S4 replacement method for signature 'Chromatograms'
dataOrigin(object) <- value
## S4 method for signature 'Chromatograms'
msLevel(object)
## S4 replacement method for signature 'Chromatograms'
msLevel(object) <- value
## S4 method for signature 'Chromatograms'
mz(object)
## S4 replacement method for signature 'Chromatograms'
mz(object) <- value
## S4 method for signature 'Chromatograms'
mzMax(object)
## S4 replacement method for signature 'Chromatograms'
mzMax(object) <- value
## S4 method for signature 'Chromatograms'
mzMin(object)
## S4 replacement method for signature 'Chromatograms'
mzMin(object) <- value
## S4 method for signature 'Chromatograms'
length(x)
## S4 method for signature 'Chromatograms'
precursorMz(object)
## S4 replacement method for signature 'Chromatograms'
precursorMz(object) <- value
## S4 method for signature 'Chromatograms'
precursorMzMin(object)
## S4 replacement method for signature 'Chromatograms'
precursorMzMin(object) <- value
## S4 method for signature 'Chromatograms'
precursorMzMax(object)
## S4 replacement method for signature 'Chromatograms'
precursorMzMax(object) <- value
## S4 method for signature 'Chromatograms'
productMz(object)
## S4 replacement method for signature 'Chromatograms'
productMz(object) <- value
## S4 method for signature 'Chromatograms'
productMzMin(object)
## S4 replacement method for signature 'Chromatograms'
productMzMin(object) <- value
## S4 method for signature 'Chromatograms'
productMzMax(object)
## S4 replacement method for signature 'Chromatograms'
productMzMax(object) <- value
## S4 method for signature 'Chromatograms'
filterChromData(
object,
variables = character(),
ranges = numeric(),
match = c("any", "all"),
keep = TRUE
)
object |
A Chromatograms object. |
columns |
A |
drop |
A |
value |
replacement value for |
x |
A Chromatograms object. |
variables |
For |
ranges |
For |
match |
For |
keep |
For |
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 the data.
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.
Philippine Louail
Chromatograms for a general description of the Chromatograms
object.
peaksData for a general description of the chromatographic peaks
data available in the object, as well as how to access, replace and
subset them.
processingQueue for more information on the queuing
of processings and parallelization for larger dataset processing.
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