xps (version 1.32.0)

PreFilter-constructor: Constructor for Class PreFilter

Description

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

Usage

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

Arguments

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.

Value

An object of type "PreFilter"

Details

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).

See Also

Filter, UniFilter

Examples

## 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)