dplyr / SummarizedExperiment compatibility layer -- half baked

gistfile1.txt

## dplyr compatibility

as.data.frame.RangedSummarizedExperiment <- 
    function(x, row.names=NULL, optional=FALSE, ...)
{
    colData <- colData(x)
    rownames(colData) <- NULL
    cbind(as.data.frame(rowRanges(x)[as.vector(row(x))]),
          as.data.frame(colData[as.vector(col(x)),, drop=FALSE]),
          sapply(assays(x), as.vector))
}

setMethod("as.data.frame", "RangedSummarizedExperiment",
    as.data.frame.RangedSummarizedExperiment)

select_.RangedSummarizedExperiment <-
    function(.data, ..., .dots)
{
    dots <- lazyeval::all_dots(.dots, ...)
    include <- c("seqnames", "start", "end", "strand")
    rows <- rowRanges(x)
    cols <- colData(x)
    vars <- select_vars_(c(include, names(mcols(rows)), names(cols)),
                         dots, include)

    mcols(rows) <- mcols(rows)[, names(mcols(rows)) %in% vars, drop=FALSE]
    cols <- cols[, names(cols) %in% vars, drop=FALSE]
    initialize(.data, rowRanges=rows, colData=cols)
}

filter_.RangedSummarizedExperiment <-
    function(.data, ..., .dots)
{
    dots <- lazyeval::all_dots(.dots, ..., all_named=TRUE)

    ## FIXME: report invalid '...'
    ## rows
    i <- seq_len(nrow(.data))
    df <- tbl_df(cbind(as.data.frame(rowRanges(.data)),
                       .__i__=seq_len(nrow(.data))))
    for (d in dots)
        tryCatch({
            i <- intersect(i, filter_(df, d)$.__i__)
        }, error=function(...) {})

    ## columns
    j <- seq_len(ncol(.data))
    df <- tbl_df(cbind(as.data.frame(colData(.data)),
                       .__j__=seq_len(ncol(.data))))
    for (d in dots)
        tryCatch({
            j <- intersect(j, filter_(df, d)$.__j__)
        }, error=function(...) {})

    .data[i, j]
}