PreFilter-class: Class PreFilter

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

Description

Class PreFilter allows to apply different filters to class ExprTreeSet, i.e. to the expression level data.frame data.

Objects from the Class

Objects can be created by calls of the form new("PreFilter", ...).
Alternatively, the contructor PreFilter can be used.

Slots

mad:

Object of class "list" describing parameters for madFilter.

cv:

Object of class "list" describing parameters for cvFilter.

variance:

Object of class "list" describing parameters for varFilter.

difference:

Object of class "list" describing parameters for diffFilter.

ratio:

Object of class "list" describing parameters for ratioFilter.

gap:

Object of class "list" describing parameters for gapFilter.

hithreshold:

Object of class "list" describing parameters for highFilter.

lothreshold:

Object of class "list" describing parameters for lowFilter.

quantile:

Object of class "list" describing parameters for quantileFilter.

prescall:

Object of class "list" describing parameters for callFilter.

numfilters:

Object of class "numeric" giving the number of filters applied.

Extends

Class "Filter", directly.

Methods

callFilter

signature(object = "PreFilter"): extracts slot prescall.

callFilter<-

signature(object = "PreFilter", value = "character"): replaces slot prescall with character vector c(cutoff, samples, condition).

cvFilter

signature(object = "PreFilter"): extracts slot cv.

cvFilter<-

signature(object = "PreFilter", value = "numeric"): replaces slot cv with numeric vector c(cutoff, trim, epsilon).

diffFilter

signature(object = "PreFilter"): extracts slot difference.

diffFilter<-

signature(object = "PreFilter", value = "numeric"): replaces slot difference with numeric vector c(cutoff, trim, epsilon).

gapFilter

signature(object = "PreFilter"): extracts slot gap.

gapFilter<-

signature(object = "PreFilter", value = "numeric"): replaces slot gap with numeric vector c(cutoff, window, trim, epsilon).

highFilter

signature(object = "PreFilter"): extracts slot hithreshold.

highFilter<-

signature(object = "PreFilter", value = "character"): replaces slot hithreshold with character vector c(cutoff, parameter, condition).

lowFilter

signature(object = "PreFilter"): extracts slot lothreshold.

lowFilter<-

signature(object = "PreFilter", value = "character"): replaces slot lothreshold with character vector c(cutoff, parameter, condition).

madFilter

signature(object = "PreFilter"): extracts slot mad.

madFilter<-

signature(object = "PreFilter", value = "numeric"): replaces slot mad with numeric vector c(cutoff, epsilon).

quantileFilter

signature(object = "PreFilter"): extracts slot quantile.

quantileFilter<-

signature(object = "PreFilter", value = "numeric"): replaces slot quantile with numeric vector c(cutoff, loquantile, hiquantile).

ratioFilter

signature(object = "PreFilter"): extracts slot ratio.

ratioFilter<-

signature(object = "PreFilter", value = "numeric"): replaces slot ratio with numeric vector c(cutoff).

varFilter

signature(object = "PreFilter"): extracts slot variance.

varFilter<-

signature(object = "PreFilter", value = "numeric"): replaces slot variance with numeric vector c(cutoff, trim, epsilon).

Author(s)

Christian Stratowa

See Also

related classes Filter, UniFilter.

Examples

## for demonstration purposes only:  initialize all pre-filters
prefltr <- new("PreFilter")
madFilter(prefltr) <- c(0.5,0.01)
cvFilter(prefltr) <- c(0.3,0.0,0.01)
varFilter(prefltr) <- c(0.6,0.02,0.01)
diffFilter(prefltr) <- c(2.2,0.0,0.01)
ratioFilter(prefltr) <- c(1.5)
gapFilter(prefltr) <- c(0.3,0.05,0.0,0.01)
lowFilter(prefltr) <- c(4.0,3,"samples")
highFilter(prefltr) <- c(14.5,75.0,"percent")
quantileFilter(prefltr) <- c(3.0, 0.05, 0.95)
callFilter(prefltr) <- c(0.02,80.0,"percent")
str(prefltr)

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