| unifilter {xps} | R Documentation |
This function applies an UniFilter to an ExprTreeSet.
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, ...)
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. |
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.
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).
Christian Stratowa
## 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)