| bgcorrect {xps} | R Documentation |
Background corrects probe intensities in an object of class DataTreeSet.
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, select = "antigenomic", exonlevel = "", verbose = TRUE) bgcorrect.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "all", exonlevel = "", verbose = TRUE) bgcorrect.mas5(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "both", exonlevel = "", verbose = TRUE) bgcorrect.rma(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", exonlevel = "", verbose = TRUE) xpsBgCorrect(object, ...)
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. |
Background corrects probe intensities in an object of class DataTreeSet.
xpsBgCorrect is the DataSet method called by function bgcorrect,
containing the same parameters.
An DataTreeSet
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="/"))
## 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))))
}
## Not run:
## examples using Affymetrix human tissue dataset (see also xps/examples/script4exon.R)
## example - exon array, e.g. HuEx-1_0-st-v2:
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
datdir <- "/Volumes/GigaDrive/CRAN/Workspaces/ROOTData"
scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na25.root",sep="/"))
data.exon <- root.data(scheme.exon, paste(datdir,"HuTissuesExon_cel.root",sep="/"))
## compute rma background
workdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Exon/hutissues/exon"
data.bg.rma <- bgcorrect(data.exon, "HuExonRMABgrd", filedir=workdir, tmpdir="",
method="rma", select="antigenomic", option="pmonly:epanechnikov",
params=c(16384), exonlevel="metacore+affx")
# or alternatively:
data.bg.rma <- bgcorrect.rma(data.exon, "HuExonRMABgrd", filedir=workdir, tmpdir="",
select="antigenomic", exonlevel="metacore+affx")
## End(Not run)