removeIntensity,Chromatogram-method {xcms} | R Documentation

## Remove intensities from chromatographic data

### Description

`removeIntensities` allows to remove intensities from chromatographic data matching certain conditions (depending on parameter `which`). The intensities are actually not removed but replaced with `NA_real_`. To actually remove the intensities (and the associated retention times) use `clean()` afterwards.

Parameter `which` allows to specify which intensities should be replaced by `NA_real_`. By default (`which = "below_threshod"` intensities below `threshold` are removed. If `x` is a `XChromatogram` or `XChromatograms` object (and hence provides also chromatographic peak definitions within the object) `which = "outside_chromPeak"` can be selected which removes any intensity which is outside the boundaries of identified chromatographic peak(s) in the chromatographic data.

Note that `filterIntensity()` might be a better approach to subset/filter chromatographic data.

### Usage

    ## S4 method for signature 'Chromatogram'
    removeIntensity(object, which = "below_threshold", threshold = 0)

    ## S4 method for signature 'MChromatograms'
    removeIntensity(object, which = "below_threshold", threshold = 0)

    ## S4 method for signature 'XChromatogram'
    removeIntensity(
      object,
      which = c("below_threshold", "outside_chromPeak"),
      threshold = 0
    )

### Arguments

`object` | an object representing chromatographic data. Can be a `Chromatogram()`, `MChromatograms()`, `XChromatogram()` or `XChromatograms()` object.
`which` | `character(1)` defining the condition to remove intensities. See description for details and options.
`threshold` | `numeric(1)` defining the threshold below which intensities are removed (if `which = "below_threshold"`).

### Value

the input object with matching intensities being replaced by `NA`.

### Author(s)

Johannes Rainer

### Examples

    chr <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
        intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))

    ## Remove all intensities below 20
    res <- removeIntensity(chr, threshold = 20)
    intensity(res)

[Package xcms version 3.16.1 Index]