Pseudobulk

pseudobulk(object, ...)

# S4 method for SingleCellExperiment
pseudobulk(object, fun = c("mean",
  "geometricMean", "median"))

Arguments

object

Object.

fun

character(1). Name of the aggregation function. Uses match.arg() internally.

...

Additional arguments.

Value

Modified object, with cells aggregated to samples, like a bulk RNA-seq dataset.

Note

Updated 2019-08-11.

Examples

data(SingleCellExperiment, package = "acidtest") ## SingleCellExperiment ==== object <- SingleCellExperiment x <- pseudobulk(object)
#> Aggregating counts using 'mean()'.
#> class: RangedSummarizedExperiment #> dim: 500 2 #> metadata(1): aggregate #> assays(1): counts #> rownames(500): gene001 gene002 ... gene499 gene500 #> rowData names(8): broadClass description ... geneName seqCoordSystem #> colnames(2): sample1 sample2 #> colData names(0):