callFilter-methods: Detection Call Filter

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

Description

Detection Call Filter.
The cutoff value defines the upper threshold for allowed detection call p-values. If e.g. the number of samples exceeding this cutoff value is greater than samples then the corresponding expression dataframe row is flagged, i.e. flag = 0.
The Detection Call Filter flags all rows with: flag = (sum(call[i] >= cutoff) >= samples)

Usage

callFilter(object)
callFilter(object, value)<-

Arguments

object	object of class PreFilter or UniFilter.
value	character vector c(cutoff, samples, condition).

Details

The method callFilter initializes the following parameters:

	cutoff:	the cutoff value for the filter:
		cutoff = 1.0: present/absent call is used.
		cutoff < 1.0: detection p-value is used as cutoff.
	samples:	this value depends on the condition used:
	condition:	condition="samples": number of samples (default):
		condition="percent": percent of samples.

Value

An initialized PreFilter or UniFilter object.

Author(s)

Christian Stratowa

Examples

## initialize PreFilter
prefltr <- PreFilter()
callFilter(prefltr) <- c(0.02,80.0,"percent")
str(prefltr)

## initialize UniFilter
unifltr <- UniFilter()
callFilter(unifltr) <- c(0.02,80.0,"percent")
str(unifltr)

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