calcPC-methods: Peakclustering into pseudospectra according to a distance...

In CAMERA: Collection of annotation related methods for mass spectrometry data

Description

A number of clustering methods exist in CAMERA. calcPC is the generic method.

Usage

  calcPC(object, method, ...)

Arguments

object	xsAnnotate-class object
method	Method to use for clustering. See details.
...	Optional arguments to be passed along

Details

This algorithms cluster peaks from a xsAnnotate object into pseudospectra according to a provided distance matrix. Therefore all peaks are transformend into a graph, with peaks as nodes and the value from the distance matrix as edges. Afterwards a graph separation algorithm is applied, which searches in the graph for clusters. See the manpages of the specific clustering algorithms for more information.

If the xsAnnotate is pregrouped, for example groupFWHM, only the already existing groups will be further processed.

The different algorithms that can be used by specifying them with the method argument. For example to use the highly connected subgraphs approach by E. Hartuv, R. Shamir, (1999), one would use: calcPC(object, method="hcs"). This is also the default, see calcPC.hcs.

Further arguments given by ... are passed through to the function implementing the method, which are most likely ajc. The parameter ajc is the peak distance matrix.

getOption("BioC")$CAMERA$findPeaks.methods returns a character vector of nicknames for the algorithms available.

The function returns a xsAnnotate object with grouping information, as list of peak indices. They are stored as object@pspectra.

See Also

calcPC.lpc calcPC.hcs xsAnnotate-class

CAMERA documentation built on Nov. 8, 2020, 4:59 p.m.