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 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 peaks data variables information can be accessed using the peaksData() function. It is also possible to access specific peaks variables using $.

peaks 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
)

## S4 method for signature 'Chromatograms'
applyProcessing(
  object,
  f = processingChunkFactor(object),
  BPPARAM = bpparam(),
  ...
)

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

Arguments

object	A Chromatograms object.
columns	For peaksData() accessor: optional character with column names (peaks variables) that should be included in the returned list of data.frame. By default, all columns are returned.
f	factor defining the grouping to split the Chromatograms object.
BPPARAM	Parallel setup configuration. See BiocParallel::bpparam() for more information.
drop	logical(1) 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.
variables	For filterPeaksData(): character vector with the names of the chromatogram variables to filter for. The list of available chromatogram 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 chromatogram data that match the condition.
FUN	For addProcessing() A function to be added to the Chromatograms object's processing queue.

Filter Peaks Variables

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

Since peaks data can be quite large, a processing queue is used to ensure efficiency. The backend data remains unchanged until the processing queue is applied (e.g., by running applyProcessing()). When calling peaksData(), the processing queue is applied to the output, but the backend data is not replaced.

The available functions to filter chromatogram data include:

• filterPeaksData(): Filters numerical peaks data variables based on the specified numerical ranges. 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.

Author(s)

Philippine Louail

See Also

Chromatograms for a general description of the Chromatograms object, and chromData for accessing,substituting and filtering chromatographic variables.

rformassspectrometry/Chromatograms documentation built on Jan. 24, 2025, 6:29 a.m.