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.: 4.00 1st Qu.: 4.00 1st Qu.: 4.00 1st Qu.: 4.00 #> Median : 14.50 Median : 16.00 Median : 15.00 Median : 15.00 #> Mean : 45.11 Mean : 43.53 Mean : 43.47 Mean : 45.32 #> 3rd Qu.: 47.00 3rd Qu.: 47.00 3rd Qu.: 48.25 3rd Qu.: 47.25 #> Max. :881.00 Max. :898.00 Max. :1110.00 Max. :1017.00 #> sample05 sample06 sample07 sample08 #> Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 4.00 1st Qu.: 4.00 1st Qu.: 4.00 #> Median : 14.00 Median : 14.00 Median : 15.00 Median : 17.00 #> Mean : 45.22 Mean : 42.80 Mean : 58.23 Mean : 56.79 #> 3rd Qu.: 48.00 3rd Qu.: 49.25 3rd Qu.: 52.25 3rd Qu.: 57.25 #> Max. :1186.00 Max. :763.00 Max. :1230.00 Max. :1143.00 #> sample09 sample10 sample11 sample12 #> Min. : 0.00 Min. : 0 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 3.00 1st Qu.: 4 1st Qu.: 3.00 1st Qu.: 3.75 #> Median : 17.00 Median : 17 Median : 16.00 Median : 17.00 #> Mean : 53.93 Mean : 57 Mean : 57.20 Mean : 57.04 #> 3rd Qu.: 53.25 3rd Qu.: 60 3rd Qu.: 57.25 3rd Qu.: 58.25 #> Max. :1041.00 Max. :972 Max. :1267.00 Max. :1147.00