probeContentGC-methods: Get G/C Content for Probes

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

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”.

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.

Value

A data.frame.

Author(s)

Christian Stratowa

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()

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