View source: R/functions-XCMSnExp.R
Replaces the raw retention times with the adjusted retention time or returns the object unchanged if none are present.
An XCMSnExp object.
Adjusted retention times are stored in parallel to the adjusted
retention times in the
applyAdjustedRtime replaces the
raw retention times (stored in the feature data (
with the adjusted retention times.
XCMSnExp with the raw retention times being replaced with the
adjusted retention time.
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
processHistory() of the
object to ensure that the processing
history is preserved.
adjustRtime() for the function to perform the alignment (retention
[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.
## 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))[] - split(rtime(xod), fromFile(xod))[], type = "l") ## And the process history still contains the settings for the alignment processHistory(xod)
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