applyAdjustedRtime: Replace raw with adjusted retention times

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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)

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.