peaksData: Chromatographic peaks data

In rformassspectrometry/Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data

Chromatographic peaks data

Description

As explained in the Chromatograms class documentation, the Chromatograms object is a container for chromatographic 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 peaks data variables information can be accessed using the peaksData() function. It is also possible to access specific peaks variables using $.

The peaks data can be accessed, replaced but also filtered/subsetted. Refer to the sections below for more details.

Usage

## S4 method for signature 'Chromatograms'
peaksData(
  object,
  columns = peaksVariables(object),
  f = processingChunkFactor(object),
  BPPARAM = bpparam(),
  drop = FALSE,
  ...
)

## S4 replacement method for signature 'Chromatograms'
peaksData(object) <- value

## S4 method for signature 'Chromatograms'
peaksVariables(object, ...)

## S4 method for signature 'Chromatograms'
rtime(object, ...)

## S4 replacement method for signature 'Chromatograms'
rtime(object) <- value

## S4 method for signature 'Chromatograms'
intensity(object, ...)

## S4 replacement method for signature 'Chromatograms'
intensity(object) <- value

## S4 method for signature 'Chromatograms'
filterPeaksData(
  object,
  variables = character(),
  ranges = numeric(),
  match = c("any", "all"),
  keep = TRUE
)

Arguments

object	A Chromatograms object.
columns	For peaksData(): optional character with column names (peaks variables) that should be included in the returned list of data.frame. By default, all columns are returned. Available variables can be found by calling peaksVariables() on the object.
f	factor defining the grouping to split the Chromatograms object.
BPPARAM	Parallel setup configuration. See BiocParallel::bpparam() for more information.
drop	logical(1) For peaksData(), default to FALSE. If TRUE, and one column is called by the user, the method returns a list of vector of the single column requested.
...	Additional arguments passed to the method.
value	For rtime() and intensity(): numeric vector with the values to replace the current values. The length of the vector must match the number of peaks data pairs in the Chromatograms object.
variables	For filterPeaksData(): character vector with the names of the peaks data variables to filter for. The list of available peaks data variables can be obtained with peaksVariables().
ranges	For filterPeaksData() : 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).
match	For filterPeaksData() : character(1) defining whether the condition has to match for all provided ranges (match = "all"; the default), or for any of them (match = "any").
keep	For filterPeaksData(): logical(1) defining whether to keep (keep = TRUE) or remove (keep = FALSE) the chromatographic peaks data that match the condition.

Filter Peaks Variables

Functions that filter a Chromatograms's peaks data (i.e., peaksData). These functions remove peaks data that do not meet the specified conditions. If a chromatogram in a Chromatograms object is filtered, only the corresponding peaks variable pairs (i.e., rows) in the peaksData are removed, while the chromatogram itself remains in the object.

The available functions to filter chromatographic peaks data include:

• filterPeaksData(): Filters numerical peaks data variables based on the specified numerical ranges parameter. This method returns the same input Chromatograms object, but the filtering step is added to the processing queue. The filtered data will be reflected when the user accesses peaksData. This function does not reduce the number of chromatograms in the object, but it removes the specified peaks data (e.g., "rtime" and "intensity" pairs) from the peaksData.

In the case of a read-only backend, (such as the ChromBackendMzR), the replacement of the peaks data is not possible. The peaks data can be filtered, but the filtered data will not be saved in the backend. This means the original mzml files will not be affected by computations performed on the Chromatograms.

Author(s)

Philippine Louail

See Also

Chromatograms for a general description of the Chromatograms object, and chromData for accessing,substituting and filtering chromatographic variables. For more information on the queuing of processings and parallelization for larger dataset processing see processingQueue.

rformassspectrometry/Chromatograms documentation built on Feb. 22, 2025, 11:28 a.m.