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 test data
    files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
        system.file('cdf/KO/ko16.CDF', package = "faahKO"),
        system.file('cdf/KO/ko18.CDF', package = "faahKO"))

    od <- readMSData(files, mode = "onDisk")

    ## Apply obiwarp retention time adjustment. We have to convert the
    ## OnDiskMSnExp first to an XCMSnExp
    xod <- as(od, "XCMSnExp")
    xod <- adjustRtime(xod, 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(od), fromFile(od))[[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 3.9.1 Index]