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
## 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)