xps (version 1.32.0)

callFilter-methods: Detection Call Filter

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).

Value

An initialized PreFilter or UniFilter object.

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):

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)