attachProbe-methods: Attach/Remove Probe Sequence and/or GC Content

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

Description

Attach/remove probe sequence and/or GC content to/from SchemeTreeSet or to slot scheme of DataTreeSet.

Usage

attachProbe(object, varlist)

attachProbeContentGC(object)

attachProbeSequence(object)

removeProbe(object)

removeProbeContentGC(object)

removeProbeSequence(object)

Arguments

object	Object of class "SchemeTreeSet" or "DataTreeSet".
varlist	names of probe tree leaves to import to slot probe.

Details

Function attachProbe exports leaves from probe tree of ROOT scheme file and and saves the data as data.frame probe of slot scheme.

Following varlist parameters are valid:

	fPosition:	probe interrogation position.
	fSequence:	probe sequence.
	fNumberGC:	number of G/C nucleotides in probe sequence.
	fTm:	probe melting temperature dependent on G/C number.
	fIsAntisense:	probe type (sense/antisense).

Function attachProbeContentGC saves fNumberGC in data.frame probe of SchemeTreeSet or in slot scheme of DataTreeSet.

Function attachProbeSequence saves fSequence in data.frame probe of SchemeTreeSet.

Function removeProbe removes probe data from SchemeTreeSet or from slot scheme of DataTreeSet and replaces data.frame probe with an empty data.frame of dim(0,0).

Value

A SchemeTreeSet object or DataTreeSet.

Note

Do not use attachProbe unless you know that your computer has sufficient RAM, especially for exon array schemes.

Author(s)

Christian Stratowa

See Also

attachMask

Examples

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

scheme.test3 <- attachProbe(scheme.test3, varlist="fSequence:fNumberGC")
dim(chipProbe(scheme.test3))
head(chipProbe(scheme.test3))

scheme.test3 <- removeProbe(scheme.test3)
dim(chipProbe(scheme.test3))

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