xps (version 1.32.0)

firma.expr: Get Expression Levels from FIRMA

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’.

Value

A data.frame.

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.

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)