| prefilter {xps} | R Documentation |
This function applies a PreFilter to an ExprTreeSet.
prefilter(xps.expr,
filename = character(0),
filedir = getwd(),
filter = NULL,
minfilters = 999,
logbase = "log2",
treename = "PreFilter",
xps.call = NULL,
verbose = TRUE)
xpsPreFilter(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 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. |
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.
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_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)