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SE2DGEList <- function(object)
# Given any SummarizedExperiment data object, extract basic information needed
# and convert it into a DGEList object
# Yunshun Chen, Gordon Smyth
# 18 March 2020. Last modified 23 March 2020.
{
if(!is(object,"SummarizedExperiment"))
stop("object is not of the SummarizedExperiment class")
if(!requireNamespace("SummarizedExperiment",quietly=TRUE))
stop("SummarizedExperiment package required but is not installed (or can't be loaded)")
# Check 'assays'
if( !("counts" %in% SummarizedExperiment::assayNames(object)) ) stop("object doesn't contain counts")
counts <- SummarizedExperiment::assay(object,"counts")
if(!is.null(rownames(object))) rownames(counts) <- rownames(object)
if(!is.null(colnames(object))) colnames(counts) <- colnames(object)
genes <- samples <- NULL
# Check 'colData'
if(ncol(SummarizedExperiment::colData(object))){
samples <- as.data.frame(SummarizedExperiment::colData(object))
}
# Check 'rowData'
if(is(SummarizedExperiment::rowRanges(object), "GRanges"))
genes <- as.data.frame(SummarizedExperiment::rowRanges(object))
else if(ncol(SummarizedExperiment::rowData(object)))
genes <- as.data.frame(SummarizedExperiment::rowData(object))
DGEList(counts=counts, samples=samples, genes=genes)
}
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