unifilter: Function for Applying an UniFilter to an ExprTreeSet

Description

This function applies an UniFilter to an ExprTreeSet.

Usage

unifilter(xps.expr, filename   = character(0), filedir    = getwd(), filter     = NULL, minfilters = 999, logbase    = "log2", group      = character(0), treename   = "UniTest", xps.fltr   = NULL, xps.call   = NULL, update     = FALSE, verbose    = TRUE)

xpsUniFilter(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 UniFilter.

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"

group

a character vector assigning the trees of xps.expr to one of two groups.

treename

tree name to be used in ROOT filter file.

xps.fltr

optional object of class FilterTreeSet.

xps.call

optional object of class CallTreeSet.

update

logical. If TRUE the existing ROOT filter file filename will be updated.

verbose

logical, if TRUE print status information.

object

object of class ExprTreeSet.

...

same arguments as function unifilter.

Value

An AnalysisTreeSet

Details

This function applies the different filters initialized with constructor UniFilter 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 pre-filtering should be done before applying function unifilter then a FilterTreeSet xps.fltr must be supplied, created with function prefilter.

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

Examples

Run this code

## 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_Test3_RMA",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_Test3_RMA.root:
# data.rma@rootfile <- paste(path.package("xps"),"rootdata/tmp_Test3RMA.root",sep="/")
# data.rma@filedir  <- paste(path.package("xps"),"rootdata",sep="/")
# 
# ## third, construct an UniFilter
# unifltr <- UniFilter(unitest=c("t.test","two.sided","none",0,0.0,FALSE,0.95,TRUE),foldchange=c(1.3,"both"),unifilter=c(0.1,"pval"))
# 
# ## finally, create an AnalysisTreeSet
# rma.ufr <- unifilter(data.rma,"tmp_Test3Unifilter",getwd(),unifltr,group=c("GrpA","GrpA","GrpB","GrpB"),verbose=FALSE)
# str(rma.ufr)
# ## End(Not run)