ppsetApply {affy}R Documentation

Apply a function over the ProbeSets in an AffyBatch

Description

Apply a function over the ProbeSets in an AffyBatch

Usage

ppsetApply(abatch, FUN, genenames = NULL, ...)

ppset.ttest(ppset, covariate, pmcorrect.fun = pmcorrect.pmonly, ...)

Arguments

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

Details

Value

Returns a list of objects, or values, as returned by the function FUN for each ProbeSet it processes.

Author(s)

Laurent Gautier <laurent@cbs.dtu.dk>

See Also

ProbeSet-class

Examples

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)
}

## create a dataset
data(affybatch.example)
abatch <- merge(affybatch.example, affybatch.example)
intensity(abatch) <- 2^jitter(log2(intensity(abatch)),1,1)
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")


[Package affy version 1.8.1 Index]