Nothing
as.data.frame.SpliceExprSet <- function(x, row.names=NA, optional=NA, ...) {
if (! is(x, "SpliceExprSet"))
stop("the argument should inherit class 'SpliceExprSet'")
spSites <- x@spliceSites
eset <- x@eset
probes <- x@probes
nc.eset <- ncol(exprs(eset))
nr.eset <- nrow(exprs(eset))
## sanity check
## (because slots of objects can be tweaked by the user)
if (nr.eset != nrow(probes@pos)) {
stop("inconsistency beetween slots 'eset' and 'probes'")
}
## build the probe position column
i.probes <- seq(1, nr.eset)
i.probes.expand <- rep(i.probes, nc.eset)
## build the 'is in type x' columns
probeOnSpSite <- isProbeOnSpliceSite(probes, spSites)
## build the probe level intensities columns
rv.eset <- local({
X <- exprs(eset)
cbind(as.data.frame(lapply(pData(eset), rep, each=nrow(X))),
exprs=c(X))
})
rv <- do.call(data.frame, c(list(begin = probes@pos[, 1][i.probes.expand],
end = probes@pos[, 2][i.probes.expand],
isintypeI = probeOnSpSite$isintypeI[i.probes.expand],
isintypeII = probeOnSpSite$isintypeII[i.probes.expand]),
lapply(rv.eset, function(x) return(x)),
lapply(probes@info, function(x, i) return(x[i]), i.probes.expand)
)
)
return(rv)
}
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