xps (version 1.32.0)

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

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.

Value

A SchemeTreeSet object or DataTreeSet.

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.

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).

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))