R/reorder_assays.R

In BarcUVa-Seq/FieldEffectCrc: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects

reorder_assays <- function(se, order=c("counts", "abundance", "length")) {
    l <- as.list(SummarizedExperiment::assays(se))
    tmp <- list()
    for (each in names(l)) {
        tmp[[each]] <- l[[each]]
    }
    for (i in seq_len(length(order))) {
        if (order[i] == "counts") {
            l[[i]] <- round(tmp[[order[i]]])
        } else {
            l[[i]] <- tmp[[order[i]]]
        }
    }
    names(l) <- order
    SummarizedExperiment::assays(se) <- l
    return(se)
}