applyAdjustedRtime {xcms} | R Documentation

## Replace raw with adjusted retention times

### Description

Replaces the raw retention times with the adjusted retention time or returns the object unchanged if none are present.

### Usage

    applyAdjustedRtime(object)

### Arguments

`object` | An XCMSnExp object.

### Details

Adjusted retention times are stored in parallel to the adjusted retention times in the `XCMSnExp`. The `applyAdjustedRtime` replaces the raw retention times (stored in the feature data (`fData` `data.frame`)) with the adjusted retention times.

### Value

A `XCMSnExp` with the raw retention times being replaced with the adjusted retention time.

### Note

Replacing the raw retention times with adjusted retention times disables the possibility to restore raw retention times using the `dropAdjustedRtime()` method. This function does not remove the retention time processing step with the settings of the alignment from the `processHistory()` of the `object` to ensure that the processing history is preserved.

### Author(s)

Johannes Rainer

### See Also

`adjustRtime()` for the function to perform the alignment (retention time correction).

    [adjustedRtime()] for the method to extract adjusted retention times from
    an [XCMSnExp] object.

    [dropAdjustedRtime] for the method to delete alignment results and to
    restore the raw retention times.

### Examples

    ## Load a test data set with detected peaks
    data(faahko_sub)
    ## Update the path to the files for the local system
    dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")

    ## Disable parallel processing for this example
    register(SerialParam())

    xod <- adjustRtime(faahko_sub, param = ObiwarpParam())

    hasAdjustedRtime(xod)

    ## Replace raw retention times with adjusted retention times.
    xod <- applyAdjustedRtime(xod)

    ## No adjusted retention times present
    hasAdjustedRtime(xod)

    ## Raw retention times have been replaced with adjusted retention times
    plot(split(rtime(faahko_sub), fromFile(faahko_sub))[[1]] -
        split(rtime(xod), fromFile(xod))[[1]], type = "l")

    ## And the process history still contains the settings for the alignment
    processHistory(xod)

[Package xcms version 3.16.1 Index]