gapFilter-methods: Gap Filter

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

This method initializes the Gap Filter.
The gapFilter looks for genes that might usefully discriminate between two groups. To do this we look for a gap in the ordered expression values. The gap should come in the central portion, thus a parameter window is defined to exclude jumps in the initial window values and the final window values.
The Gap Filter flags all rows with: flag = ((gap[i+1] - gap[i])/mean >= cutoff)

gapFilter(object)
gapFilter(object, value)<-

Arguments

object	object of class PreFilter.
value	numeric vector c(cutoff, window, trim, epsilon).

Details

The method gapFilter initializes the following parameters:

	cutoff:	the cutoff level for the filter.
	window:	trim value for the ordered expression levels (default is window=0.05).
	trim:	the trim value for trimmed mean (default is trim=0).
	epsilon:	value to replace mean (default is epsilon=0.01):
		epsilon > 0: replace mean=0 with epsilon.
		epsilon = 0: always set mean=1.

Note, that for epsilon = 0 the filter flags all rows with: (gap[i+1] - gap[i]) >= cutoff

Value

An initialized PreFilter object.

Author(s)

Christian Stratowa

Examples

prefltr <- PreFilter()
gapFilter(prefltr) <- c(0.3,0.05,0.0,0.01)
str(prefltr)

xps documentation built on Nov. 8, 2020, 6 p.m.