filterResult.AssocTestResultRanges <-
function(object, cutoff=0.05,
filterBy=c("p.value", "p.value.adj", "p.value.resampled",
"p.value.resampled.adj"))
{
filterBy <- match.arg(filterBy)
if (is.null(mcols(object)[[filterBy]]))
stop("column '", filterBy, "' missing", call.=FALSE)
object[which(mcols(object)[[filterBy]] <= cutoff)]
}
setMethod("filterResult", signature(object="AssocTestResultRanges"),
filterResult.AssocTestResultRanges)
filterResult.GRanges <- function(object, cutoff=0.1)
{
if (is.null(mcols(object)$weight.contribution))
stop("'object' has no metadata column 'weight.contribution'",
call.=FALSE)
else
object[which(mcols(object)$weight.contribution >= cutoff)]
}
setMethod("filterResult", signature(object="GRanges"),
filterResult.GRanges)
setMethod("filterResult", signature(object="GRangesList"),
function(object, cutoff=0.1)
GRangesList(lapply(object, filterResult.GRanges, cutoff=cutoff)))
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