xps (version 1.32.0)

metaProbesets: Create MetaProbeset File for APT

Description

Create MetaProbeset File for APT function “apt-probeset-summarize”.

Usage

metaProbesets(xps.scheme, infile = character(0), outfile = character(0), exonlevel="metacore")

Arguments

xps.scheme

exon SchemeTreeSet.

infile

Name of file containing exon transcript\_cluster\_ids.

outfile

Name of resulting file containing meta probeset definitions.

exonlevel

exon annotation level determining which probes should be used.

Value

None.

Details

This function allows to create a metaprobeset file for APT function “apt-probeset-summarize” to be used with option “-m”. The infile must contain exon transcript\_cluster\_ids, one per line, e.g. one can export the rownames(data.rma) The resulting file may be useful if you want to compare results created with xps to results created with APT function “apt-probeset-summarize”.

Examples

## Not run: 
# ## first, load ROOT exon scheme file:
# scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"
# scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na25.root",sep="/"))
# 
# metaProbesets(scheme.exon,"metacore.txt","metacoreList.mps","metacore")
# ## End(Not run)