bpmapToProbeAnno: Creating a probeAnno object
In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description Usage Arguments Author(s) Examples

This function allows the user to create a probeAnno environment that holds the mapping between probes on the array and their genomic match position(s). The function takes an Affymetrix bpmap file as input.

1	bpmapToProbeAnno(bpmap, verbose=T, uniqueSeq=T)

`bpmap`	Either a list, created by the function readBpmap() from the affy package. Or a path to the bpmap file.
`verbose`	should the progress be printed out?
`uniqueSeq`	If TRUE, probes sequences that occur more than once on the chip (and consequently match several positions on the genome) are set to 1 in the probeAnno object. Unique probes are set to 0. If false, all probes are set to 0. To identify all unique and multiple matching probes, a remapping of the probes to the genome is recommended.

Benedikt Zacher zacher@lmb.uni-muenchen.de

##
# dataPath <- system.file("extdata", package="Starr")
# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))

# probeAnnoChr1 <- bpmapToProbeAnno(bpmapChr1)

Starr documentation built on April 28, 2020, 7:52 p.m.