matchAffyProbes {altcdfenvs} | R Documentation |
Match the individual probes on an Affymetrix array to arbitrary targets.
mmProbes(probes) matchAffyProbes(probes, targets, chip_type, matchmm = TRUE, selectMatches = function(x) which(countIndex(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 sparce 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 <- readFASTA(filename) targets <- unlist(lapply(fasta.seq, "[[", "seq")) names(targets) <- lapply(fasta.seq, "[[", "desc") names(targets) <- sub("^>.+\\|(NM[^ \\|]+|Hs[^ \\|]+)\\|? .+$", "\\1", names(targets)) m <- matchAffyProbes(hgu133aprobe, targets, "HG-U133A")