xps (version 1.32.0)

lowFilter-methods: Lower Threshold Filter

Description

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

Usage

lowFilter(object) lowFilter(object, value)<-

Arguments

object

object of class PreFilter.

value

character vector c(cutoff, parameter, condition).

Value

An initialized PreFilter object.

Details

The method lowFilter initializes the following parameters:

	cutoff:
the lower 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.

Examples

prefltr <- PreFilter()
lowFilter(prefltr) <- c(4.0,3,"samples")
str(prefltr)