matchAffyProbes: Match the probes on an Affymetrix array
In altcdfenvs: alternative CDF environments (aka probeset mappings)

Description Usage Arguments Details Value Author(s) See Also Examples

Match the individual probes on an Affymetrix array to arbitrary targets.

mmProbes(probes)

matchAffyProbes(probes, targets, chip_type,
                matchmm = TRUE,
                selectMatches = function(x) which(elementNROWS(x) > 0),
                ...)

`probes`	a `probetable` object
`targets`	a vector of references
`chip_type`	a name for the chip type.
`matchmm`	whether to match MM probes or not
`selectMatches`	a function to select matches (see Details).
`...`	further arguments to be passed to `matchPDict`.

The matching is performed by the function matchPDict. The man page for that function will indicate what are the options it accepts.

In the case where a large number targets are given, like when each target represents a possible mRNA, is it expected to have a largely sparse incidence matrix, that is a low number of probes matching every target. For that reason, only the index of matching probes are associated with each given target, with the function selectMatches giving the definition of what are matching probes. The default function just count anything matching, but the user can specify a more stringent definition if wanted.

mmProbes returns a vector of MM probe sequences.

matchAffyProbes returns an instance of AffyProbesMatch-class.

Laurent Gautier

matchPDict for details on how the matching is performed, AffyProbesMatch-class and buildCdfEnv.biostrings

library(hgu133aprobe)

filename <- system.file("exampleData", "sample.fasta",
                        package="altcdfenvs")

fasta.seq <- readDNAStringSet(filename)

targets <- as.character(fasta.seq)
names(targets) <- sub("^>.+\\|(NM[^ \\|]+|Hs[^ \\|]+)\\| ? .+$", "",
                      names(targets))

m <- matchAffyProbes(hgu133aprobe,
                     targets,
                     "HG-U133A")