validData-methods: Extract Subset of Data

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

Description

Extracts a subset of valid data from data.frame data.

Usage

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

Arguments

object	object of class DataTreeSet, ExprTreeSet or CallTreeSet.
which	type of probes to be returned for DataTreeSet, otherwise name of column containing unit name.
unitID	optional vector of UNIT_IDs.
unittype	character vector, “transcript” or “probeset”.

Details

For class DataTreeSet and expression arrays, validData returns all the perfect match or mismatch probes on the arrays the object represents as data.frame, i.e. which can have the following values:

	pm:	perfect match probes.
	mm:	mismatch probes.
	both:	both perfect match and mismatch probes.

For class DataTreeSet and exon arrays, validData 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.
	all:	combination of above.
	genomic:	genomic background probes.
	antigenomic:	antigenomic background probes.

For class ExprTreeSet validData returns the valid expression levels from slot data with unit names as row names, usually the probeset IDs stored in column which="UnitName".

For class CallTreeSet validData returns the valid detection call p-values from slot data with unit names as row names, usually the probeset IDs stored in column which="UnitName".

Value

A data.frame.

Author(s)

Christian Stratowa

See Also

pm, mm, validExpr, validCall

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