prefilter {xps}R Documentation

Function for Applying a PreFilter to an ExprTreeSet

Description

This function applies a PreFilter to an ExprTreeSet.

Usage

prefilter(xps.expr,
          filename   = character(0),
          filedir    = getwd(),
          filter     = NULL,
          minfilters = 999,
          logbase    = "log2",
          treename   = "PreFilter",
          xps.call   = NULL,
          verbose    = TRUE)

xpsPreFilter(object, ...)

Arguments

xps.expr object of class ExprTreeSet.
filename file name of ROOT filter file.
filedir system directory where ROOT filter file should be stored.
filter object of class PreFilter.
minfilters minimum number of initialized filter methods to satisfy (default is all filters).
logbase convert data to logarithm of base: "0", "log", "log2" (default), "log10"
treename tree name to be used in ROOT filter file.
xps.call optional object of class CallTreeSet.
verbose logical, if TRUE print status information.
object object of class ExprTreeSet.
... same arguments as function prefilter.

Details

This function applies the different filters initialized with constructor PreFilter to the ExprTreeSet xps.expr.

Slot minfilters determines the minimum number of initialized filters, which must be satisfied so that the mask is set to flag=1. For minfilters=1 at least one filter must be satisfied, equivalent to logical ‘OR’; for minfilters=999 all filters must be satisfied, equivalent to logical ‘AND’.

If method callFilter was initialized with constructor PreFilter then CallTreeSet xps.call must be supplied, usually created with function mas5.call.

Value

A FilterTreeSet

Author(s)

Christian Stratowa

See Also

PreFilter, unifilter

Examples

## first, load ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## second, create an ExprTreeSet
data.rma <- rma(data.test3,"tmp_TestRMA",tmpdir="",background="pmonly",normalize=TRUE,verbose=FALSE)
## note: do not copy/paste this code, it is necessary only because R CMD check fails since it does not find tmp_TestRMA.root:
data.rma@rootfile <- paste(.path.package("xps"),"rootdata/tmp_Test3RMA.root",sep="/")
data.rma@filedir  <- paste(.path.package("xps"),"rootdata",sep="/")

## third, construct a PreFilter
prefltr <- PreFilter(mad=c(0.5,0.01),lothreshold=c(6.0,0.02,"mean"),hithreshold=c(10.5,80.0,"percent"))

## finally, create a FilterTreeSet
rma.pfr <- prefilter(data.rma,"tmp_Test3Prefilter",getwd(),prefltr,2,verbose=FALSE)
str(rma.pfr)

[Package xps version 1.2.10 Index]