Correct retention time from different samples

To correct differences between retention times between different samples, a number of of methods exist in XCMS. retcor is the generic method.

Methods

object = "xcmsSet"

retcor(object, ...)

Arguments

object

xcmsSet-class object

method

Method to use for retention time correction. See details.

...

Optional arguments to be passed along

Details

Different algorithms can be used by specifying them with the method argument. For example to use the approach described by Smith et al (2006) one would use: retcor(object, method="loess"). This is also the default.

Further arguments given by ... are passed through to the function implementing the method.

A character vector of nicknames for the algorithms available is returned by getOption("BioC")$xcms$retcor.methods. If the nickname of a method is called "loess", the help page for that specific method can be accessed with ?retcor.loess.

Value

An xcmsSet object with corrected retntion times.

See also

retcor.loess retcor.obiwarp xcmsSet-class,