xps (version 1.32.0)

pm-methods: Methods for accessing perfect matches and mismatches

Description

Methods for accessing perfect match (PM) and mismatch (MM) probes.

Usage

pm(object, which = "pm", unitID = NULL, unittype = "transcript")

mm(object, which = "mm", unitID = NULL, unittype = "transcript")

Arguments

object

object of class DataTreeSet.

which

type of perfect match or mismatch probes to be returned.

unitID

optional vector of UNIT_IDs.

unittype

character vector, “transcript” or “probeset”.

Value

A data.frame.

Details

For expression arrays all the perfect match (pm) or mismatch (mm) probes on the arrays the object represents are returned as data.frame.

For exon arrays, pm returns the probes of the different exon levels as data.frame, i.e. which can have one of the following values:

	core:
probesets supported by RefSeq and full-length GenBank transcripts.
metacore:	core meta-probesets.
	extended:
probesets with other cDNA support.
metaextended:	extended meta-probesets.
	full:
probesets supported by gene predictions only.
metafull:	full meta-probesets.

For whole genome arrays, pm returns the probes of the different exon levels as data.frame, i.e. which can have one of the following values:

	core:
probesets with category ‘unique’ and ‘mixed’.
metacore:	probesets with category ‘unique’ only.

For exon/genome arrays, mm returns the background probes as data.frame, i.e. which is either “genomic” or “antigenomic”.

See Also

validData

Examples

## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## need to attach scheme mask and probe intensities
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)

pm <- pm(data.test3)
mm <- mm(data.test3)
head(pm)
head(mm)

## need to convert Affy ID to UNIT_ID first
id <- transcriptID2unitID(schemeSet(data.test3), transcriptID="100084_at", as.list=FALSE)
pm <- pm(data.test3, unitID=id)
mm <- mm(data.test3, unitID=id)
head(pm)
head(mm)

## optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)