callFilter-methods {xps}R Documentation

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).

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)

[Package xps version 1.2.10 Index]