indexUnits-methods: Unit Locations

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

Description

Returns a data.frame or list with locations of the probes in each probe set.

Usage

indexUnits(object, which = "", unitID = NULL, unittype = "transcript", as.list = TRUE, data = NULL)

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

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

Arguments

object	Object of class "DataTreeSet".
which	type of probes to be used, for details see validData.
unitID	optional vector of UNIT_IDs.
unittype	character vector, “transcript” or “probeset”.
as.list	if TRUE a list will be returned (default is data.frame).
data	optional data.frame containing (x,y)-coordinates.

Details

Function indexUnits returns a data.frame or list with locations of the probes in each probe set.

By default a data.frame for selected unitIDs or all unitIDs (unitID="*") will be returned with columns <UNIT_ID, X, Y, XY>. Here "XY" are the selected rows of slot data.

For as.list=TRUE a list of unitIDs will be returned containing the selected rows "XY". The names of the elements in the list returned are the UNIT_IDs.

For unitID=NULL a vector of data rows "XY" will be returned.

For expression arrays which can be one of "pm", "mm", or "both". Alternatively, functions pmindex and mmindex can be used for PM probes or MM probes, respectively.

For exon arrays which is described in validData. However, in this case slot data must contain the (x,y)-coordinates of the probesetIDs.

Value

A list or data.frame.

Author(s)

Christian Stratowa

See Also

unitID2transcriptID, unitID2probesetID

Examples

## first, load 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="/"))

## dataXY not attached
id <- indexUnits(data.test3, which="pm", unitID=c(34,36,122))
id

## dataXY attached (only necessary for whole genome and exon arrays)
data.test3 <- attachDataXY(data.test3)
xy <- treeData(data.test3)
id <- indexUnits(data.test3, which="pm", unitID=c(34,36,122), data=xy)
id
id <- indexUnits(data.test3, which="", unitID=c(34,36,122), data=xy)
id
id <- indexUnits(data.test3, which="", unitID=34, as.list=FALSE, data=xy)
id
data.test3 <- removeDataXY(data.test3)

rm(scheme.test3, data.test3)
gc()

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