Integer counts

integerCounts(object, ...)

# S4 method for Matrix
integerCounts(object)

# S4 method for SummarizedExperiment
integerCounts(object)

# S4 method for matrix
integerCounts(object)

Arguments

object

Object.

...

Additional arguments.

Value

Matrix. Typically matrix or Matrix class.

Note

Updated 2020-12-21.

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

Examples

data(RangedSummarizedExperiment, package = "AcidTest") ## SummarizedExperiment ==== object <- RangedSummarizedExperiment x <- integerCounts(object) class(x)
#> [1] "matrix" "array"
#> [1] TRUE
#> sample01 sample02 sample03 sample04 #> Min. : 0.00 Min. : 0.0 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 5.00 1st Qu.: 5.0 1st Qu.: 5.00 1st Qu.: 5.00 #> Median : 17.00 Median : 16.0 Median : 15.00 Median : 17.00 #> Mean : 39.34 Mean : 39.3 Mean : 39.13 Mean : 40.01 #> 3rd Qu.: 41.00 3rd Qu.: 39.0 3rd Qu.: 44.25 3rd Qu.: 43.25 #> Max. :686.00 Max. :679.0 Max. :816.00 Max. :788.00 #> sample05 sample06 sample07 sample08 #> Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 5.00 1st Qu.: 5.00 1st Qu.: 4.00 1st Qu.: 4.00 #> Median : 17.50 Median : 18.00 Median : 18.50 Median : 16.00 #> Mean : 40.07 Mean : 40.23 Mean : 49.63 Mean : 48.50 #> 3rd Qu.: 43.00 3rd Qu.: 41.00 3rd Qu.: 44.00 3rd Qu.: 46.25 #> Max. :687.00 Max. :600.00 Max. :899.00 Max. :858.00 #> sample09 sample10 sample11 sample12 #> Min. : 0.00 Min. : 0.00 Min. : 0.00 Min. : 0.00 #> 1st Qu.: 4.00 1st Qu.: 5.00 1st Qu.: 4.00 1st Qu.: 4.00 #> Median : 17.00 Median : 17.00 Median : 15.00 Median : 17.00 #> Mean : 47.93 Mean : 49.83 Mean : 48.15 Mean : 49.25 #> 3rd Qu.: 51.00 3rd Qu.: 48.00 3rd Qu.: 46.50 3rd Qu.: 47.00 #> Max. :929.00 Max. :1251.00 Max. :861.00 Max. :1148.00