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
## 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)