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 Matrix class.

Note

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

Updated 2019-12-04.

Examples

data(RangedSummarizedExperiment, package = "AcidTest") ## SummarizedExperiment ==== object <- RangedSummarizedExperiment x <- counts(object) summary(x)
#> sample01 sample02 #> Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 5.00 #> Median : 17.00 Median : 15.00 #> Mean : 41.76 Mean : 45.26 #> 3rd Qu.: 41.25 3rd Qu.: 48.25 #> Max. :719.00 Max. :1407.00 #> sample03 sample04 #> Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 4.00 #> Median : 14.00 Median : 15.00 #> Mean : 42.95 Mean : 43.41 #> 3rd Qu.: 44.25 3rd Qu.: 45.00 #> Max. :1301.00 Max. :1658.00 #> sample05 sample06 #> Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 4.00 #> Median : 15.00 Median : 16.00 #> Mean : 45.93 Mean : 45.36 #> 3rd Qu.: 46.00 3rd Qu.: 49.25 #> Max. :1102.00 Max. :1257.00 #> sample07 sample08 #> Min. : 0.00 Min. : 0.00 #> 1st Qu.: 3.75 1st Qu.: 3.00 #> Median : 15.00 Median : 16.00 #> Mean : 54.74 Mean : 57.66 #> 3rd Qu.: 53.25 3rd Qu.: 56.00 #> Max. :1167.00 Max. :1285.00 #> sample09 sample10 #> Min. : 0.00 Min. : 0.00 #> 1st Qu.: 3.00 1st Qu.: 4.00 #> Median : 15.00 Median : 15.00 #> Mean : 56.08 Mean : 57.66 #> 3rd Qu.: 55.25 3rd Qu.: 56.75 #> Max. :1249.00 Max. :1024.00 #> sample11 sample12 #> Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 3.75 #> Median : 15.50 Median : 17.00 #> Mean : 57.02 Mean : 59.53 #> 3rd Qu.: 53.25 3rd Qu.: 57.25 #> Max. :1081.00 Max. :1385.00