Group peaks from different samples together

A number of grouping (or alignment) methods exist in XCMS. group is the generic method.

Methods

object = "xcmsSet"

group(object, ...)

Arguments

object

xcmsSet-class object

method

Method to use for grouping. 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 density-based approach described by Smith et al (2006) one would use: group(object, method="density"). 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")$xcms$group.methods. If the nickname of a method is called "mzClust", the help page for that specific method can be accessed with ?group.mzClust.

Value

An xcmsSet object with peak group assignments and statistics.

See also

group.density group.mzClust group.nearest xcmsSet-class,