probeSequence-methods: Get Probe Sequence

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

Description

Get probe sequences for all or selected UNIT_IDs.

Usage

probeSequence(object, unitID = NULL)

Arguments

object	Object of class "SchemeTreeSet" or "DataTreeSet".
unitID	optional vector of UNIT_IDs.

Details

Function probeSequence returns a data.frame containing column “ProbeSequence” for all or selected the UNIT_ID(s).

Value

A data.frame.

Author(s)

Christian Stratowa

See Also

probeContentGC

Examples

## load ROOT scheme file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
scheme.test3 <- attachProbeSequence(scheme.test3)

## get UNIT_ID for probeset ID
id <- probesetID2unitID(scheme.test3, "100084_at")

## get GC content
seq <- probeSequence(scheme.test3, unitID=id)
head(seq)

scheme.test3 <- removeProbeSequence(scheme.test3)

rm(scheme.test3)
gc()

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