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Fill spectra data with columns for missing core variables

Source: R/MsBackend-functions.R
fillCoreSpectraVariables.Rd

fillCoreSpectraVariables() fills a provided data.frame with columns for eventually missing core spectra variables. The missing core variables are added as new columns with missing values (NA) of the correct data type. Use coreSpectraVariables() to list the set of core variables and their data types.

Usage

fillCoreSpectraVariables(
  x = data.frame(),
  columns = names(coreSpectraVariables())
)

Arguments

x

data.frame or DataFrame with potentially present core variable columns.

columns

character with the names of the (core) spectra variables that should be added if not already present in x. Defaults to columns = names(coreSpectraVariables()).

Value

input data frame x with missing core variables added (with the correct data type).

Examples


## Define a data frame
a <- data.frame(msLevel = c(1L, 1L, 2L), other_column = "b")

## Add missing core chromatogram variables to this data frame
fillCoreSpectraVariables(a)
#> Warning: corrupt data frame: columns will be truncated or padded with NAs
#>   msLevel other_column rtime acquisitionNum scanIndex dataStorage dataOrigin
#> 1       1            b    NA             NA        NA        <NA>       <NA>
#> 2       1            b    NA             NA        NA        <NA>       <NA>
#> 3       2            b    NA             NA        NA        <NA>       <NA>
#>   centroided smoothed polarity precScanNum precursorMz precursorIntensity
#> 1         NA       NA       NA          NA          NA                 NA
#> 2         NA       NA       NA          NA          NA                 NA
#> 3         NA       NA       NA          NA          NA                 NA
#>   precursorCharge collisionEnergy isolationWindowLowerMz
#> 1              NA              NA                     NA
#> 2              NA              NA                     NA
#> 3              NA              NA                     NA
#>   isolationWindowTargetMz isolationWindowUpperMz
#> 1                      NA                     NA
#> 2                      NA                     NA
#> 3                      NA                     NA
#>                                                                mz
#> 1 <S4 class ‘SimpleNumericList’ [package “IRanges”] with 4 slots>
#> 2                                                            <NA>
#> 3                                                            <NA>
#>                                                         intensity
#> 1 <S4 class ‘SimpleNumericList’ [package “IRanges”] with 4 slots>
#> 2                                                            <NA>
#> 3                                                            <NA>

## The data.frame thus contains columns for all core spectra
## variables in the respective expected data type (but filled with
## missing values).