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rowsum.DGEList <- function (x, group, reorder=FALSE, na.rm=FALSE, ...)
# Sum counts by groups of rows/genes and
# return a DGEList with a row for each level of 'group'.
# Gordon Smyth
# Created 22 Feb 2018. Last modified 23 May 2018.
{
isdupgrp <- duplicated(group)
x2 <- x[!isdupgrp,]
x2$counts <- rowsum(x$counts,group=group,reorder=FALSE,na.rm=na.rm,...)
if(!is.null(x$genes)) {
# Keep those columns of x$genes that contain group-level annotation
no <- logical(nrow(x))
isdupall <- vapply(x$genes,duplicated,no)[isdupgrp,,drop=FALSE]
isgenelevel <- (colSums(isdupall) == nrow(isdupall))
x2$genes <- x2$genes[,isgenelevel,drop=FALSE]
row.names(x2$genes) <- row.names(x2$counts)
}
if(reorder) {
o <- order(row.names(x2))
x2 <- x2[o,]
}
x2
}
rowsum.SummarizedExperiment <- function(x, group, reorder=FALSE, na.rm=FALSE, ...)
# Created 03 April 2020. Last modified 03 April 2020.
{
x <- SE2DGEList(x)
rowsum.DGEList(x, group=group, reorder=reorder, na.rm=na.rm, ...)
}
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