metaProbesets: Create MetaProbeset File for APT

Description Usage Arguments Details Value Author(s) Examples

View source: R/utils.R

Description

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

Usage

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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

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## 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)

xps documentation built on Nov. 1, 2018, 2:29 a.m.