ppsetApply {affy} | R Documentation |
Apply a function over the ProbeSets in an AffyBatch
ppsetApply(abatch, FUN, genenames = NULL, ...) ppset.ttest(ppset, covariate, pmcorrect.fun = pmcorrect.pmonly, ...)
abatch |
An object inheriting from AffyBatch . |
ppset |
An object of class ProbeSet . |
covariate |
the name a covariate in the slot phenoData . |
pmcorrect.fun |
a function to corrrect PM intensities |
FUN |
A function working on a ProbeSet |
genenames |
A list of Affymetrix probesets ids to work with. All
probe set ids used when NULL . |
... |
Optional parameters to the function FUN |
Returns a list
of objects, or values, as returned by the
function FUN
for each ProbeSet
it processes.
Laurent Gautier <laurent@cbs.dtu.dk>
ppset.ttest <- function(ppset, covariate, pmcorrect.fun = pmcorrect.pmonly, ...) { probes <- do.call("pmcorrect.fun", list(ppset)) my.ttest <- function(x) { y <- split(x, get(covariate)) t.test(y[[1]], y[[2]])$p.value } r <- apply(probes, 1, my.ttest) return(r) } ## craft a dataset data(affybatch.example) abatch <- merge(affybatch.example, affybatch.example) intensity(abatch) <- jitter(intensity(abatch)) chip.variate <- c("a", "b", "a", "a", "b", "a", "a") pData(abatch) <- data.frame(whatever = chip.variate) ## run a test over _all_ probes. all.ttest <- ppsetApply(abatch, ppset.ttest, covariate="whatever")