Removes class/annotation information from a matrix of candidate markers that appear in the fData.

Removes annotation information that contain more that a certain number/percentage of proteins

filterMaxMarkers(object, n, p = 0.2, fcol = "GOAnnotations", verbose = TRUE)

Arguments

object: An instance of class MSnSet.
n: Maximum number of proteins allowed per class/information term.
p: Maximum percentage of proteins per column. Default is 0.2 i.e. remove columns that have information for greater than 20 of the total number of proteins in the dataset (note: this is useful for example, if information is GO terms, for removing very general and uninformative terms).
fcol: The name of the matrix of marker information. Default is GOAnnotations.
verbose: Number of marker candidates retained after filtering.

An updated MSnSet