# ---------------------------------------------------------------------------- #
#' resTable
#'
#' Function that reads multiple find_circ output files and returns a
#' SummarizedExperiment object
#'
#'
#' @param se a SummarizedExperiment object
#' @param ... other arguments
#'
#' @return returns a data.table
#'
#'
#' @docType methods
#' @rdname resTable-methods
#'
#' @export
setGeneric("resTable",
function(se,
...)
standardGeneric("resTable"))
#' @aliases resTable,RangedSummarizedExperiment-method
#' @rdname resTable-methods
setMethod("resTable",
signature("RangedSummarizedExperiment"),
definition = function(se, ...) {
DT <- data.table(as.data.frame(rowRanges(se)))
setnames(DT, "seqnames", "chr")
for (i in 1:length(colData(se)$sample)) {
DT <- cbind(DT, sapply(names(assays(se)),
function(x) assays(se)[[x]][, i]))
setnames(DT, tail(names(DT), length(assays(se))),
paste0(colData(se)$sample[i], "_",
tail(names(DT), length(assays(se)))))
}
return(DT)
})
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