xps (version 1.32.0)

gapFilter-methods: Gap Filter

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).

Value

An initialized PreFilter object.

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.

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

Examples

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