attachCall-methods: Attach/Remove Detecion Call Measures

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

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.

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).

Value

A CallTreeSet object.

Note

Do not use attachCall and attachPVal unless you know that your computer has sufficient RAM, especially when using exon arrays. It may be advisible to use a subset of treenames only.

Author(s)

Christian Stratowa

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()

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