Count matrix.

counts(object, ...)

counts(object, ...) <- value

# S4 method for SummarizedExperiment
counts(object)

# S4 method for SummarizedExperiment,matrix
counts(object) <- value

# S4 method for SummarizedExperiment,Matrix
counts(object) <- value

Arguments

object

Object.

value

Value to assign.

...

Additional arguments.

Value

Matrix. Typically matrix or sparseMatrix class.

Note

For a SummarizedExperiment object, "counts" must be explicitly defined in assayNames.

Updated 2019-08-06.

Examples

data(RangedSummarizedExperiment, package = "acidtest") rse <- RangedSummarizedExperiment ## SummarizedExperiment ==== x <- counts(rse) summary(x)
#> sample01 sample02 sample03 sample04 #> Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 3.00 1st Qu.: 3.00 1st Qu.: 4.00 1st Qu.: 3.00 #> Median : 13.00 Median : 14.00 Median : 13.00 Median : 14.00 #> Mean : 38.28 Mean : 39.02 Mean : 38.09 Mean : 37.91 #> 3rd Qu.: 39.25 3rd Qu.: 38.00 3rd Qu.: 36.00 3rd Qu.: 38.00 #> Max. :978.00 Max. :1074.00 Max. :988.00 Max. :827.00 #> sample05 sample06 sample07 sample08 #> Min. : 0.0 Min. : 0.00 Min. : 0.00 Min. : 0.0 #> 1st Qu.: 4.0 1st Qu.: 4.00 1st Qu.: 4.00 1st Qu.: 4.0 #> Median : 14.0 Median : 13.00 Median : 14.50 Median : 14.0 #> Mean : 38.9 Mean : 38.89 Mean : 59.59 Mean : 60.1 #> 3rd Qu.: 39.0 3rd Qu.: 32.25 3rd Qu.: 41.25 3rd Qu.: 37.0 #> Max. :1165.0 Max. :919.00 Max. :2396.00 Max. :3725.0 #> sample09 sample10 sample11 sample12 #> Min. : 0.00 Min. : 0.00 Min. : 0.0 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 3.00 1st Qu.: 4.0 1st Qu.: 3.00 #> Median : 13.00 Median : 14.00 Median : 15.0 Median : 14.00 #> Mean : 56.29 Mean : 55.58 Mean : 58.7 Mean : 49.98 #> 3rd Qu.: 40.00 3rd Qu.: 36.00 3rd Qu.: 42.0 3rd Qu.: 41.00 #> Max. :3469.00 Max. :2596.00 Max. :3588.0 Max. :1555.00