Description Usage Arguments Details Value Note Author(s) See Also Examples
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.
1 | applyAdjustedRtime(object)
|
object |
An XCMSnExp object. |
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.
A 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
the processHistory()
of the object
to ensure that the processing
history is preserved.
Johannes Rainer
adjustRtime()
for the function to perform the alignment (retention
time correction).
1 2 3 4 5 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ## 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)
|
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