PreFilter-class {xps} | R Documentation

## Class PreFilter

### 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)

[Package xps version 1.4.10 Index]