probesetID2unitID-methods: Conversion between Probeset IDs and UnitIDs

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

Description

Convert probeset IDs and transcript IDs to internal UNIT_IDs and vice verse.

Usage

probesetID2unitID(object, probesetID = NULL, as.list = TRUE)

transcriptID2unitID(object, transcriptID = NULL, as.list = TRUE)

unitID2probesetID(object, unitID = NULL, as.list = TRUE)

unitID2transcriptID(object, unitID = NULL, as.list = TRUE)

Arguments

object	Object of class "SchemeTreeSet" or "DataTreeSet".
probesetID	optional vector of probeset IDs.
transcriptID	optional vector of transcript IDs.
unitID	optional vector of UNIT_IDs.
as.list	if TRUE a list will be returned (default is data.frame).

Details

Functions probesetID2unitID and transcriptID2unitID return the UNIT_ID(s) for all or selected probeset IDs or transcript IDs, respectively.

Conversely, functions unitID2probesetID and unitID2transcriptID return the probeset IDs or transcript IDs, respectively, for all or selected UNIT_IDs. . For expression arrays the functions for probeset IDs and transcript IDs return identical IDs. . For exon arrays the functions for probeset IDs and transcript IDs return the probeset_id(s) or transcript_cluster_id(s), respectivley.

By default a list is returned, however for as.list=FALSE a character vector of IDs is returned.

Value

A list or character vector.

Author(s)

Christian Stratowa

See Also

unitID2transcriptID, unitID2probesetID

Examples

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

## unitNames not attached
id <- unitID2probesetID(scheme.test3, c(2,34,229))
id

## unitNames attached
scheme.test3 <- attachUnitNames(scheme.test3)
id <- probesetID2unitID(scheme.test3, c("PA1178_oprH_at","AFFX-Bt_eIF-4E_3_at","100084_at"))
id
scheme.test3 <- removeUnitNames(scheme.test3)

rm(scheme.test3)
gc()

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