PreFilter-constructor: Constructor for Class PreFilter
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Value Note Author(s) See Also Examples

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

PreFilter(mad         = character(),
          cv          = character(),
          variance    = character(),
          difference  = character(),
          ratio       = character(),
          gap         = character(),
          lothreshold = character(),
          hithreshold = character(),
          quantile    = character(),
          prescall    = character())

`mad`	`"character"` vector describing parameters for `madFilter`.
`cv`	`"character"` vector describing parameters for `cvFilter`.
`variance`	`"character"` vector describing parameters for `varFilter`.
`difference`	`"character"` vector describing parameters for `diffFilter`.
`ratio`	`"character"` vector describing parameters for `ratioFilter`.
`gap`	`"character"` vector describing parameters for `gapFilter`.
`lothreshold`	`"character"` vector describing parameters for `lowFilter`.
`hithreshold`	`"character"` vector describing parameters for `highFilter`.
`quantile`	`"character"` vector describing parameters for `quantileFilter`.
`prescall`	`"character"` vector describing parameters for `callFilter`.

The PreFilter constructor allows to apply the following filters to class ExprTreeSet:

	`mad`:	character vector c(cutoff,epsilon).
	`cv`:	character vector c(cutoff,trim,epsilon).
	`variance`:	character vector c(cutoff,trim,epsilon).
	`difference`:	character vector c(cutoff,trim,epsilon).
	`ratio`:	character vector c(cutoff).
	`gap`:	character vector c(cutoff,window,trim,epsilon).
	`lothreshold`:	character vector c(cutoff,parameter,condition).
	`hithreshold`:	character vector c(cutoff,parameter,condition).
	`quantile`:	character vector c(cutoff,loquantile,hiquantile).
	`prescall`:	character vector c(cutoff,samples,condition).

An object of type "PreFilter"

Function PreFilter is used as constructor for class PreFilter so that the user need not know details for creating S4 classes.

Christian Stratowa

Filter, UniFilter

## fill character vectors within constructor
prefltr <- PreFilter(mad=c(0.5,0.01), prescall=c(0.002, 6,"samples"),
                     lothreshold=c(6.0,0.02,"mean"), hithreshold=c(10.5,80.0,"percent"))
str(prefltr)

## alternatively add character vectors as methods after creation of constructor
prefltr <- PreFilter()
madFilter(prefltr) <- c(0.5,0.01)
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")
str(prefltr)