Replace raw with adjusted retention times

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 or XcmsExperiment object.

Value

An XCMSnExp or XcmsExperiment object with the raw (original) retention times being replaced with the adjusted retention time.

Details

Adjusted retention times are stored in parallel to the adjusted retention times in XCMSnExp or XcmsExperiment objects. The applyAdjustedRtime replaces the raw (original) retention times with the adjusted retention times.

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.

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.

Author

Johannes Rainer

Examples

## Load a test data set with detected peaks
library(MSnbase)
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())
#> Sample number 2 used as center sample.
#> Aligning ko15.CDF against ko16.CDF ... 
#> OK
#> Aligning ko18.CDF against ko16.CDF ... 
#> OK
#> Applying retention time adjustment to the identified chromatographic peaks ... 
#> OK

hasAdjustedRtime(xod)
#> [1] TRUE

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

## No adjusted retention times present
hasAdjustedRtime(xod)
#> [1] FALSE

## 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)
#> [[1]]
#> Object of class "XProcessHistory"
#>  type: Peak detection 
#>  date: Thu Mar 14 11:42:34 2024 
#>  info:  
#>  fileIndex: 1,2,3 
#>  Parameter class: CentWaveParam 
#>  MS level(s) 1 
#> 
#> [[2]]
#> Object of class "XProcessHistory"
#>  type: Retention time correction 
#>  date: Mon Apr 22 14:33:55 2024 
#>  info:  
#>  fileIndex: 1,2,3 
#>  Parameter class: ObiwarpParam 
#>  MS level(s) 1 
#>