prefilter: Function for Applying a PreFilter to an ExprTreeSet

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

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

## Not run: 
## 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)

## End(Not run)

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