unifilter: Function for Applying an UniFilter 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 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.

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.

Value

An AnalysisTreeSet

Note

Internally, slot group will be converted to integer values using as.integer(as.factor(group)), thus group=c("GrpA","GrpA","GrpB","GrpB") will result in a fold-change of fc=mean(GrpB)/mean(GrpA).

Author(s)

Christian Stratowa

See Also

UniFilter, prefilter

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_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)

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