firma.expr: Get Expression Levels from FIRMA

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Extracts FIRMA expression levels from data.frame data.

Usage

firma.expr(xps.data,
           probeset = NULL,
           option   = "probeset")

Arguments

xps.data	object of class ExprTreeSet.
probeset	transcriptID or probesetID or NULL.
option	option determining the probeset type for which to extract expression levels, one of ‘transcript’, ‘probeset’, ‘exon’.

Details

Function firma.expr returns the expression levels from slot data for a given probeset, or for all probesets or transcripts in case of probeset=NULL. Row names will be the Affymetrix transcriptIDs, probesetIDs or exonIDs, respectively, dependent on the selected option.

Value

A data.frame.

Note

For option="probeset" parameter probeset should usually be the transcriptID in order to get the expression levels for all probesetIDs of the corresponding transcriptID.

Author(s)

Christian Stratowa

See Also

firma

Examples

## Not run: 
## get transcript expression levels for all transcripts or for transcript=2429277
expr.firma <- firma.expr(sub.firma.ps, probeset=NULL, option="transcript")
expr.firma <- firma.expr(sub.firma.ps, probeset=2429277, option="transcript")

## get probeset expression levels for all probeset or for probeset=2429278
expr.firma <- firma.expr(sub.firma.ps, probeset=NULL, option="probeset")
expr.firma <- firma.expr(sub.firma.ps, probeset=2429278, option="probeset")

## get probeset expression levels for all probesets corresponding to transcript=2429277
expr.firma <- firma.expr(sub.firma.ps, probeset=2429277, option="probeset")

## End(Not run)

xps documentation built on Nov. 8, 2020, 6 p.m.