presCall-methods: Get/Set Present Call Values

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Get/set present call values from/for class CallTreeSet.

Usage

presCall(object)
presCall(object, treenames = NULL) <- value

pvalData(object)
pvalData(object, treenames = NULL) <- value

Arguments

object	object of class CallTreeSet.
treenames	character vector containing optional tree names to be used as subset.
value	data.frame containing present call values.

Details

Get the p-values from slot data or present calls from slot detcall, or set slot data or detcall, respectively, to value.

Method presCall returns the present calls from slot detcall as data.frame, while replacement method presCall<- allows to replace slot detcall with a data.frame.

Method pvalData returns the p-values from slot data as data.frame, while replacement method pvalData<- allows to replace slot data with a data.frame.

In order to create an CallTreeSet containing only a subset of e.g. slot data, first export slot data using method pvalData, create a character vector containing only treenames to be used in the subset, and then use replacement method pvalData<- to replace slot data with the subset. Slots treenames and numtrees will be updated automatically for pvalData<- but not for presCall<-.

Note: When creating character vector treenames it is sufficient to use the name part of the tree name w/o the extension.

Note: If you do not want to replace your current object, create first a copy of type CallTreeSet by simply writing newobj <- oldobj, and use newobj for replacement.

Author(s)

Christian Stratowa

See Also

exprs

Examples

## Not run: 
## 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="/"))

## create an CallTreeSet
call.mas5 <- mas5.call(data.test3,"tmp_TestMAS5Call",tmpdir="",verbose=FALSE)

## get p-values
value <- pvalData(call.mas5)

## selected treenames only
treenames <- c("TestA2", "TestB1")

## make a copy of your object if you do not want to replace it
subset.call <- call.mas5

## replace slot data with subset
exprs(subset.call, treenames) <- value
str(subset.call)

## End(Not run)

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