metaProbesets {xps}R Documentation

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.

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”.

Value

None.

Author(s)

Christian Stratowa

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)

[Package xps version 1.2.10 Index]