xps (version 1.32.0)

probeContentGC-methods: Get G/C Content for Probes

Description

Get G/C content for all or selected UNIT_IDs.

Usage

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

Arguments

object

Object of class "SchemeTreeSet" or "DataTreeSet".

which

type of probes to be used, for details see validData.

unitID

optional vector of UNIT_IDs.

unittype

character vector, one of “transcript”, “probeset”.

Value

A data.frame.

Details

Function probeContentGC returns a data.frame containing columns “Mask” and “ContentGC” for all or selected the UNIT_ID(s).

For exon arrays the type of UNIT_ID(s) depends on unittype.

See Also

probeSequence

Examples

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

## get UNIT_ID for probeset IDs
id <- probesetID2unitID(scheme.test3, c("PA1178_oprH_at","AFFX-Bt_eIF-4E_3_at","100084_at"))

## get GC content
gc <- probeContentGC(scheme.test3, unitID=id)
head(gc)

scheme.test3 <- removeProbeContentGC(scheme.test3)

rm(scheme.test3)
gc()