altcdfenvs (version 2.34.0)

matchAffyProbes: Match the probes on an Affymetrix array

Description

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

Usage

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

Arguments

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.

Value

mmProbes returns a vector of MM probe sequences.matchAffyProbes returns an instance of AffyProbesMatch-class.

Details

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.

See Also

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

Examples

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")