bpmapToProbeAnno {Starr} | R Documentation |
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.
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)