highFilter-methods: Upper Threshold Filter

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

Description

This method initializes the Upper Threshold Filter.
The cutoff value defines the upper threshold for allowed expression levels. If e.g. the number of samples exceeding this cutoff value is greater than parameter then the corresponding dataframe row is flagged, i.e. flag = 0.
The Upper Threshold Filter flags all rows with: flag = (sum(expression[i] <= cutoff) >= parameter)

Usage

highFilter(object)
highFilter(object, value)<-

Arguments

object	object of class PreFilter.
value	character vector c(cutoff, parameter, condition).

Details

The method highFilter initializes the following parameters:

	cutoff:	the upper threshold level for the filter.
	parameter:	this value depends on the condition used:
	condition:	condition="samples": number of samples (default):
		condition="percent": percent of samples.
		condition="mean": mean value of samples.
		condition="percentile": percentile of samples.

Value

An initialized PreFilter object.

Author(s)

Christian Stratowa

Examples

prefltr <- PreFilter()
highFilter(prefltr) <- c(14.5,75.0,"percent")
str(prefltr)

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