pm-methods: Methods for accessing perfect matches and mismatches

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

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”.

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.
	affx:	standard AFFX controls.

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.
	affx:	standard AFFX controls.

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

Value

A data.frame.

Author(s)

Christian Stratowa

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)

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