xps (version 1.32.0)

attachCall-methods: Attach/Remove Detecion Call Measures

Description

Attach/remove detection call and detection p-value to/from CallTreeSet.

Usage

attachCall(object, treenames = "*")

attachPVal(object, treenames = "*")

removeCall(object)

removePVal(object)

Arguments

object

Object of class "CallTreeSet".

treenames

Object of class "list" representing the names of the ROOT call trees.

Value

A CallTreeSet object.

Details

By default detection calls will be saved in class CallTreeSet in slots data and detcall, respectively, since usually the data.frames obtained as result of e.g. mas5.call are of reasonable size. However, when computing many arrays, especially exon arrays at probeset levels, it may be better to compute detection calls with slot add.data=FALSE thus avoiding memory problems. In this case, functions attachCall and attachPVal allow to fill slots detcall and data, respectively, on demand.

attachCall exports detection calls from call trees from ROOT call file and and saves as data.frame detcall. treenames is a vector of tree names to attach; for treenames="*" all trees from slot treenames will be exported and detection calls attached as data.frame detcall.

attachPVal exports detection p-values from call trees from ROOT call file and and saves as data.frame data. treenames is a vector of tree names to attach; for treenames="*" all trees from slot treenames will be exported and detection p-values attached as data.frame data.

removeCall removes detection calls from CallTreeSet and replaces data.frame detcall with an empty data.frame of dim(0,0).

removePVal removes detection p-values from CallTreeSet and replaces data.frame data with an empty data.frame of dim(0,0).

See Also

attachExpr, removeExpr

Examples

## 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="/"))

## MAS5 detection call
call.mas5 <- mas5.call(data.test3,"tmp_Test3Call0",tmpdir="",add.data=FALSE,verbose=FALSE)

## attach data
call.mas5 <- attachPVal(call.mas5)
call.mas5 <- attachCall(call.mas5)

## get data.frames
pval.mas5 <- pvalData(call.mas5)
pres.mas5 <- presCall(call.mas5)
head(pval.mas5)
head(pres.mas5)

## remove data
call.mas5 <- removePVal(call.mas5)
call.mas5 <- removeCall(call.mas5)

rm(scheme.test3, data.test3)
gc()