Merging, combining and splitting Chromatograms

Various functions are available to combine or split data from one or more Chromatograms objects. These are:

• c() and concatenateChromatograms(): combines several Chromatograms objects into a single object. The resulting Chromatograms contains all data from all individual Chromatograms, i.e. the union of all their chromatograms variables. Concatenation will fail if the processing queue of any of the Chromatograms objects is not empty or if different backends are used for the Chromatograms objects. In such cases it is suggested to first change the backends of all Chromatograms to the same type of backend (using the ProtGenerics::setBackend() function) and to eventually (if needed) apply the processing queue using the ProtGenerics::applyProcessing() function.

• split(): splits the Chromatograms object based on a provided grouping factor returning a list of Chromatograms objects.

concatenateChromatograms(x, ...)

# S4 method for class 'Chromatograms'
c(x, ...)

# S4 method for class 'Chromatograms,ANY'
split(x, f, drop = FALSE, ...)

Arguments

x

A Chromatograms object.

...

For c() and concatenateChromatograms(): Chromatograms objects or a list of Chromatograms objects.

f

factor defining the grouping to split the Chromatograms object.

drop

For split(): not considered.

Value

• c() and concatenateChromatograms(): a single Chromatograms object containing the data from all input objects.

• split(): a list of Chromatograms objects.

Examples

## Create two Chromatograms objects
cdata1 <- data.frame(
    msLevel = c(1L, 1L),
    mz = c(112.2, 123.3),
    dataOrigin = c("file1", "file1")
)
pdata1 <- list(
    data.frame(rtime = c(1.0, 2.0, 3.0), intensity = c(100, 200, 150)),
    data.frame(rtime = c(1.0, 2.0, 3.0), intensity = c(80, 120, 90))
)
chr1 <- Chromatograms(
    ChromBackendMemory(),
    chromData = cdata1,
    peaksData = pdata1
)

cdata2 <- data.frame(
    msLevel = c(2L, 2L),
    mz = c(134.4, 145.5),
    dataOrigin = c("file2", "file2")
)
pdata2 <- list(
    data.frame(rtime = c(4.0, 5.0, 6.0), intensity = c(300, 400, 350)),
    data.frame(rtime = c(4.0, 5.0, 6.0), intensity = c(200, 250, 180))
)
chr2 <- Chromatograms(
    ChromBackendMemory(),
    chromData = cdata2,
    peaksData = pdata2
)

## Combine using c()
chr_combined <- c(chr1, chr2)
chr_combined
#> Chromatographic data (Chromatograms) with 4 chromatograms in a ChromBackendMemory backend:
#>   chromIndex msLevel    mz
#> 1         NA       1 112.2
#> 2         NA       1 123.3
#> 3         NA       2 134.4
#> 4         NA       2 145.5
#> ... 4 more  chromatogram variables/columns
#> ... 2 peaksData variables
#> Processing:
#>  Merged 2 Chromatograms into one [Thu Mar  5 13:35:28 2026] 

## Combine using concatenateChromatograms
chr_combined2 <- concatenateChromatograms(chr1, chr2)

## Combine a list of Chromatograms
chr_list <- list(chr1, chr2)
chr_combined3 <- concatenateChromatograms(chr_list)

## Split by msLevel
chr_split <- split(chr_combined, f = chr_combined$msLevel)
chr_split
#> $`1`
#> Chromatographic data (Chromatograms) with 2 chromatograms in a ChromBackendMemory backend:
#>   chromIndex msLevel    mz
#> 1         NA       1 112.2
#> 2         NA       1 123.3
#> ... 2 more  chromatogram variables/columns
#> ... 2 peaksData variables
#> Processing:
#>  Merged 2 Chromatograms into one [Thu Mar  5 13:35:28 2026] 
#> 
#> $`2`
#> Chromatographic data (Chromatograms) with 2 chromatograms in a ChromBackendMemory backend:
#>   chromIndex msLevel    mz
#> 3         NA       2 134.4
#> 4         NA       2 145.5
#> ... 2 more  chromatogram variables/columns
#> ... 2 peaksData variables
#> Processing:
#>  Merged 2 Chromatograms into one [Thu Mar  5 13:35:28 2026] 
#>