inst/scripts/coerce-functions-Ex.R

In Bioconductor/RaggedExperiment: Representation of Sparse Experiments and Assays Across Samples

x <- RaggedExperiment(GRangesList(
    GRanges(c("A:1-5", "A:4-6", "A:10-15"), score=1:3),
    GRanges(c("A:1-5", "B:1-3"), score=4:5)
))

## sparseSummarizedExperiment

sse <- sparseSummarizedExperiment(x)
assay(sse)
rowRanges(sse)

## compactSummarizedExperiment

cse <- compactSummarizedExperiment(x)
assay(cse)
rowRanges(cse)

## disjoinSummarizedExperiment

disjoinAssay(x, lengths)
dse <- disjoinSummarizedExperiment(x, lengths)
assay(dse)
rowRanges(dse)

## qreduceSummarizedExperiment

x <- RaggedExperiment(GRangesList(
    GRanges(c("A:1-3", "A:4-5", "A:10-15"), score=1:3),
    GRanges(c("A:4-5", "B:1-3"), score=4:5)
))
query <- GRanges(c("A:1-2", "A:4-5", "B:1-5"))

weightedmean <- function(scores, ranges, qranges)
{
    ## weighted average score per query range
    ## the weight corresponds to the size of the overlap of each
    ## overlapping subject range with the corresponding query range
    isects <- pintersect(ranges, qranges)
    sum(scores * width(isects)) / sum(width(isects))
}

qreduceAssay(x, query, weightedmean)
qse <- qreduceSummarizedExperiment(x, query, weightedmean)
assay(qse)
rowRanges(qse)