Compute column/row sums of a matrix-like object, for groups of rows/columns

rowsum() computes column sums across rows of a numeric matrix-like object for each level of a grouping variable.

colsum() computes row sums across columns of a numeric matrix-like object for each level of a grouping variable.

NOTE: This man page is for the rowsum and colsum S4 generic functions defined in the S4Arrays package. See ?base::rowsum for the default rowsum() method (defined in the base package). Bioconductor packages can define specific methods for objects (typically matrix-like) not supported by the default methods.

Usage

rowsum(x, group, reorder=TRUE, ...)

colsum(x, group, reorder=TRUE, ...)

Arguments

x

A numeric matrix-like object.

group, reorder, ...

See ?base::rowsum for a description of these arguments.

Value

See ?base::rowsum for the value returned by the default method.

The default colsum() method simply does t(rowsum(t(x), group, reorder=reorder, ...)).

Specific methods defined in Bioconductor packages should behave as consistently as possible with the default methods.

See also

• base::rowsum for the default rowsum method.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• rowsum,DelayedMatrix-method in the DelayedArray package for an example of a specific rowsum method (defined for DelayedMatrix objects).

Examples

rowsum  # note the dispatch on the 'x' arg only
#> new("standardGeneric", .Data = function (x, group, reorder = TRUE, 
#>     ...) 
#> standardGeneric("rowsum"), generic = "rowsum", package = "S4Arrays", 
#>     group = list(), valueClass = character(0), signature = "x", 
#>     default = new("derivedDefaultMethod", .Data = function (x, 
#>         group, reorder = TRUE, ...) 
#>     UseMethod("rowsum"), target = new("signature", .Data = "ANY", 
#>         names = "x", package = "methods"), defined = new("signature", 
#>         .Data = "ANY", names = "x", package = "methods"), generic = "rowsum"), 
#>     skeleton = (new("derivedDefaultMethod", .Data = function (x, 
#>         group, reorder = TRUE, ...) 
#>     UseMethod("rowsum"), target = new("signature", .Data = "ANY", 
#>         names = "x", package = "methods"), defined = new("signature", 
#>         .Data = "ANY", names = "x", package = "methods"), generic = "rowsum"))(x, 
#>         group, reorder, ...))
#> <bytecode: 0x55f5867809b0>
#> <environment: 0x55f58677d698>
#> attr(,"generic")
#> [1] "rowsum"
#> attr(,"generic")attr(,"package")
#> [1] "S4Arrays"
#> attr(,"package")
#> [1] "S4Arrays"
#> attr(,"group")
#> list()
#> attr(,"valueClass")
#> character(0)
#> attr(,"signature")
#> [1] "x"
#> attr(,"default")
#> Method Definition (Class "derivedDefaultMethod"):
#> 
#> function (x, group, reorder = TRUE, ...) 
#> UseMethod("rowsum")
#> <bytecode: 0x55f5867785c0>
#> <environment: namespace:base>
#> 
#> Signatures:
#>         x    
#> target  "ANY"
#> defined "ANY"
#> attr(,"skeleton")
#> (new("derivedDefaultMethod", .Data = function (x, group, reorder = TRUE, 
#>     ...) 
#> UseMethod("rowsum"), target = new("signature", .Data = "ANY", 
#>     names = "x", package = "methods"), defined = new("signature", 
#>     .Data = "ANY", names = "x", package = "methods"), generic = "rowsum"))(x, 
#>     group, reorder, ...)
#> attr(,"class")
#> [1] "standardGeneric"
#> attr(,"class")attr(,"package")
#> [1] "methods"
showMethods("rowsum")
#> Function: rowsum (package S4Arrays)
#> x="ANY"
#> x="DelayedMatrix"
#> x="SparseMatrix"
#> x="dsparseMatrix"
#> 
selectMethod("rowsum", "ANY")     # the default rowsum() method
#> new("derivedDefaultMethod", .Data = function (x, group, reorder = TRUE, 
#>     ...) 
#> UseMethod("rowsum"), target = new("signature", .Data = "ANY", 
#>     names = "x", package = "methods"), defined = new("signature", 
#>     .Data = "ANY", names = "x", package = "methods"), generic = "rowsum")
#> <bytecode: 0x55f5867842e8>
#> <environment: namespace:base>
#> attr(,"target")
#> An object of class “signature”
#>     x 
#> "ANY" 
#> attr(,"defined")
#> An object of class “signature”
#>     x 
#> "ANY" 
#> attr(,"generic")
#> [1] "rowsum"
#> attr(,"generic")attr(,"package")
#> [1] "base"
#> attr(,"class")
#> [1] "derivedDefaultMethod"
#> attr(,"class")attr(,"package")
#> [1] "methods"

colsum  # note the dispatch on the 'x' arg only
#> new("standardGeneric", .Data = function (x, group, reorder = TRUE, 
#>     ...) 
#> standardGeneric("colsum"), generic = "colsum", package = "S4Arrays", 
#>     group = list(), valueClass = character(0), signature = "x", 
#>     default = NULL, skeleton = (function (x, group, reorder = TRUE, 
#>         ...) 
#>     stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
#>         "colsum"), domain = NA))(x, group, reorder, ...))
#> <bytecode: 0x55f584883e68>
#> <environment: 0x55f58488bee8>
#> attr(,"generic")
#> [1] "colsum"
#> attr(,"generic")attr(,"package")
#> [1] "S4Arrays"
#> attr(,"package")
#> [1] "S4Arrays"
#> attr(,"group")
#> list()
#> attr(,"valueClass")
#> character(0)
#> attr(,"signature")
#> [1] "x"
#> attr(,"default")
#> `\001NULL\001`
#> attr(,"skeleton")
#> (function (x, group, reorder = TRUE, ...) 
#> stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
#>     "colsum"), domain = NA))(x, group, reorder, ...)
#> attr(,"class")
#> [1] "standardGeneric"
#> attr(,"class")attr(,"package")
#> [1] "methods"
showMethods("colsum")
#> Function: colsum (package S4Arrays)
#> x="ANY"
#> x="DelayedMatrix"
#> x="SparseMatrix"
#> x="dsparseMatrix"
#> x="matrix"
#> 
selectMethod("colsum", "ANY")     # the default colsum() method
#> new("MethodDefinition", .Data = function (x, group, reorder = TRUE, 
#>     ...) 
#> t(rowsum(t(x), group, reorder = reorder, ...)), target = new("signature", 
#>     .Data = "ANY", names = "x", package = "methods"), defined = new("signature", 
#>     .Data = "ANY", names = "x", package = "methods"), generic = "colsum")
#> <bytecode: 0x55f5848755e0>
#> <environment: namespace:S4Arrays>
#> attr(,"target")
#> An object of class “signature”
#>     x 
#> "ANY" 
#> attr(,"defined")
#> An object of class “signature”
#>     x 
#> "ANY" 
#> attr(,"generic")
#> [1] "colsum"
#> attr(,"generic")attr(,"package")
#> [1] "S4Arrays"
#> attr(,"class")
#> [1] "MethodDefinition"
#> attr(,"class")attr(,"package")
#> [1] "methods"
selectMethod("colsum", "matrix")  # colsum() method for ordinary matrices
#> new("MethodDefinition", .Data = function (x, group, reorder = TRUE, 
#>     ...) 
#> .fast_colsum(x, group, reorder = reorder, ...), target = new("signature", 
#>     .Data = "matrix", names = "x", package = "methods"), defined = new("signature", 
#>     .Data = "matrix", names = "x", package = "methods"), generic = "colsum")
#> <bytecode: 0x55f584875ea0>
#> <environment: namespace:S4Arrays>
#> attr(,"target")
#> An object of class “signature”
#>        x 
#> "matrix" 
#> attr(,"defined")
#> An object of class “signature”
#>        x 
#> "matrix" 
#> attr(,"generic")
#> [1] "colsum"
#> attr(,"generic")attr(,"package")
#> [1] "S4Arrays"
#> attr(,"class")
#> [1] "MethodDefinition"
#> attr(,"class")attr(,"package")
#> [1] "methods"