Integer counts
Usage
integerCounts(object, ...)
# S4 method for Matrix
integerCounts(object)
# S4 method for SummarizedExperiment
integerCounts(object, assay = "counts")
# S4 method for matrix
integerCounts(object)Note
Updated 2021-09-11.
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"
is.integer(x)
#> [1] TRUE
summary(x)
#> 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