bgcorrect {xps}R Documentation

Background Correction

Description

Background corrects probe intensities in an object of class DataTreeSet.

Usage

bgcorrect(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", method = character(0), option = character(0), exonlevel = "", params = list(), verbose = TRUE)

bgcorrect.gc(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", select = "antigenomic", verbose = TRUE)

bgcorrect.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", verbose = TRUE)

bgcorrect.mas5(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", verbose = TRUE)

bgcorrect.rma(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", verbose = TRUE)

xpsBgCorrect(object, ...)

Arguments

xps.data object of class DataTreeSet.
filename file name of ROOT data file.
filedir system directory where ROOT data file should be stored.
tmpdir optional temporary directory where temporary ROOT files should be stored.
update logical. If TRUE the existing ROOT data file filename will be updated.
select type of probes to select for background correction.
method background method to use.
option type of background correction to use.
exonlevel exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
params vector of parameters for background method.
verbose logical, if TRUE print status information.
object object of class DataSet.
... the arguments described above.

Details

Background corrects probe intensities in an object of class DataTreeSet.

xpsBgCorrect is the DataSet method called by function bgcorrect, containing the same parameters.

Value

An DataTreeSet

Author(s)

Christian Stratowa

See Also

express

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="/"))

## MAS4 sector background
data.bg.mas4 <- bgcorrect.mas4(data.test3,"tmp_Test3MAS4Bgrd",filedir=getwd(),tmpdir="",verbose=FALSE)

## need to attach background intensities
data.bg.mas4 <- attachBgrd(data.bg.mas4)

## get data.frame
bg.mas4 <- validBgrd(data.bg.mas4)
head(bg.mas4)

## plot images
if (interactive()) {
image.dev(data.bg.mas4,bg=TRUE,col=rainbow(32))
image(matrix(bg.mas4[,1], ncol=ncols(schemeSet(data.bg.mas4)), nrow=nrows(schemeSet(data.bg.mas4))))
}

[Package xps version 1.2.10 Index]