Count matrix.

counts(object, ...)

counts(object, ...) <- value

# S4 method for SummarizedExperiment
counts(object)

# S4 method for SummarizedExperiment
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.

Examples

data(rse, package = "acidtest") x <- counts(rse) summary(x)
#> sample01 sample02 sample03 sample04 #> Min. : 0.00 Min. : 0.0 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 4.0 1st Qu.: 4.00 1st Qu.: 3.75 #> Median : 14.00 Median : 16.0 Median : 16.00 Median : 16.00 #> Mean : 39.51 Mean : 41.4 Mean : 41.03 Mean : 40.38 #> 3rd Qu.: 38.00 3rd Qu.: 37.0 3rd Qu.: 38.00 3rd Qu.: 38.25 #> Max. :768.00 Max. :1013.0 Max. :1350.00 Max. :998.00 #> sample05 sample06 sample07 sample08 #> Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 6.00 1st Qu.: 4.00 1st Qu.: 3.00 1st Qu.: 4.00 #> Median : 16.00 Median : 12.00 Median : 12.00 Median : 14.00 #> Mean : 41.21 Mean : 44.89 Mean : 48.32 Mean : 43.38 #> 3rd Qu.: 37.00 3rd Qu.: 38.00 3rd Qu.: 43.00 3rd Qu.: 43.00 #> Max. :1074.00 Max. :1596.00 Max. :1926.00 Max. :1237.00 #> sample09 sample10 sample11 sample12 #> Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 3.75 1st Qu.: 4.00 1st Qu.: 4.00 #> Median : 15.00 Median : 13.50 Median : 16.00 Median : 15.00 #> Mean : 49.96 Mean : 51.08 Mean : 50.04 Mean : 49.83 #> 3rd Qu.: 47.00 3rd Qu.: 40.25 3rd Qu.: 44.50 3rd Qu.: 46.25 #> Max. :1840.00 Max. :1513.00 Max. :2076.00 Max. :1235.00