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Chromatographic Peaks Metadata.

Source: R/Chromatograms-chromData.R
chromData.Rd

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.

Usage

# 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'
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
)

Arguments

object

A Chromatograms object.

columns

A character vector of chromatograms variables to extract.

drop

A logical indicating whether to drop dimensions when extracting a single variable.

value

replacement value for <- methods. See individual method description or expected data type.

x

A Chromatograms object.

variables

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().

ranges

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).

match

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.

keep

For filterChromData(): logical(1) defining whether to keep (keep = TRUE) or remove (keep = FALSE) the chromatogram data that match the condition.

Value

Refer to the individual function description for information on the return value.

Chromatograms variables and accessor functions

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.

Filter Chromatograms variables

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.

See also

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.

Author

Philippine Louail

Examples


# Create a Chromatograms object
cdata <- data.frame(
    msLevel = c(1L, 1L, 1L),
    mz = c(112.2, 123.3, 134.4),
    chromIndex = c(1L, 2L, 3L)
)

be <- backendInitialize(new("ChromBackendMemory"), chromData = cdata)

chr <- Chromatograms(be)

# Access chromatograms variables
chromData(chr)
#>   msLevel    mz chromIndex collisionEnergy dataOrigin mzMin mzMax precursorMz
#> 1       1 112.2          1              NA       <NA>    NA    NA          NA
#> 2       1 123.3          2              NA       <NA>    NA    NA          NA
#> 3       1 134.4          3              NA       <NA>    NA    NA          NA
#>   precursorMzMin precursorMzMax productMz productMzMin productMzMax
#> 1             NA             NA        NA           NA           NA
#> 2             NA             NA        NA           NA           NA
#> 3             NA             NA        NA           NA           NA

# Access specific chromatograms variables
chromData(chr, columns = "msLevel")
#>   msLevel
#> 1       1
#> 2       1
#> 3       1

msLevel(chr)
#> [1] 1 1 1

# Replace chromatograms variables
msLevel(chr) <- c(1L, 2L, 2L)

# Filter chromatograms variables
filterChromData(chr,
    variables = "msLevel", ranges = c(1L, 1L),
    keep = FALSE
)
#> Chromatographic data (Chromatograms) with 2 chromatograms in a ChromBackendMemory backend:
#>   chromIndex msLevel    mz
#> 2          2       2 123.3
#> 3          3       2 134.4
#> ... 10 more  chromatogram variables/columns
#> ... 2 peaksData variables