express {xps}R Documentation

Compute expression levels from raw data

Description

This function allows to combine different algorithms to compute expression levels, or to return the result for different algorithms only.

Usage

express(xps.data,
        filename = character(),
        filedir = getwd(),
        tmpdir = "",
        update = FALSE,
      # background correction
        bgcorrect.method = NULL,
        bgcorrect.select = character(),
        bgcorrect.option = character(),
        bgcorrect.params = list(),
      # normalization
        normalize.method = NULL,
        normalize.select = character(),
        normalize.option = character(),
        normalize.logbase = character(),
        normalize.params = list(),
      # expression values
        summarize.method = NULL,
        summarize.select = character(),
        summarize.option = character(),
        summarize.logbase = character(),
        summarize.params = list(),
      # reference values
        reference.index  = 0,
        reference.method = "mean",
        reference.params = list(0),
      # misc.
        exonlevel  = "",
        xps.scheme = NULL,
        add.data   = TRUE,
        verbose    = TRUE)

xpsPreprocess(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.
bgcorrect.method background method to use.
bgcorrect.select type of probes to select for background correction.
bgcorrect.option type of background correction to use.
bgcorrect.params vector of parameters for background method.
normalize.method normalization method to use.
normalize.select type of probes to select for normalization.
normalize.option normalization option.
normalize.logbase logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’.
normalize.params vector of parameters for normalization method.
summarize.method summarization method to use.
summarize.select type of probes to select for summarization.
summarize.option option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.
summarize.logbase logarithm base as character, one of ‘0’, ‘log’, ‘log2’, ‘log10’.
summarize.params vector of parameters for summarization method.
reference.index index of reference tree to use, or 0.
reference.method for refindex=0, either trimmed mean or median of trees.
reference.params vector of parameters for reference method.
exonlevel exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
xps.scheme optional alternative SchemeSet.
add.data logical. If TRUE expression data will be included as slot data.
verbose logical, if TRUE print status information.
object object of class DataSet.
... the arguments described above.

Details

This function allows to combine different algorithms to compute expression levels, or to return the result for different algorithms only.

xpsPreprocess is the DataSet method called by function express, containing the same parameters.

Value

An object of type DataTreeSet or ExprTreeSet.

Author(s)

Christian Stratowa

See Also

bgcorrect, normalize, summarize

Examples

## load existing 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="/"))

## compute rma with a single call to express()
expr.rma <- express(data.test3,"tmp_Test3Exprs",filedir=getwd(),tmpdir="",update=FALSE,
            bgcorrect.method="rma",bgcorrect.select="none",bgcorrect.option="pmonly:epanechnikov",bgcorrect.params=c(16384),
            normalize.method="quantile",normalize.select="pmonly",normalize.option="transcript:together:none",normalize.logbase="0",normalize.params=c(0.0),
            summarize.method="medianpolish",summarize.select="pmonly",summarize.option="transcript",summarize.logbase="log2",summarize.params=c(10, 0.01, 1.0),
            verbose=FALSE)

## get expression data.frame
expr <- exprs(expr.rma)
head(expr)

## plot expression levels
if (interactive()) {
boxplot(expr.rma)
boxplot(log2(expr[,3:6]))
}

[Package xps version 1.2.10 Index]