S4Vectors: aggregate-methods – R documentation

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S4Vectors

aggregate-methods

Compute summary statistics of subsets of vector-like objects

Description

The S4Vectors package defines aggregate methods for Vector, Rle, and List objects.

Usage

## S4 method for signature 'Vector'
aggregate(x, by, FUN, start=NULL, end=NULL, width=NULL,
          frequency=NULL, delta=NULL, ..., simplify=TRUE)

## S4 method for signature 'Rle'
aggregate(x, by, FUN, start=NULL, end=NULL, width=NULL,
          frequency=NULL, delta=NULL, ..., simplify=TRUE)

## S4 method for signature 'List'
aggregate(x, by, FUN, start=NULL, end=NULL, width=NULL,
          frequency=NULL, delta=NULL, ..., simplify=TRUE)

Arguments

`x`	A Vector, Rle, or List object.
`by`	An object with `start`, `end`, and `width` methods. If `x` is a List object, the `by` parameter can be a IntegerRangesList object to aggregate within the list elements rather than across them. When `by` is a IntegerRangesList object, the output is either a SimpleAtomicList object, if possible, or a SimpleList object, if not.
`FUN`	The function, found via `match.fun`, to be applied to each subset of `x`.
`start, end, width`	The start, end, and width of the subsets. If `by` is missing, then two of the three must be supplied and have the same length.
`frequency, delta`	Optional arguments that specify the sampling frequency and increment within the subsets (in the same fashion as `window` from the stats package does).
`...`	Optional arguments to `FUN`.
`simplify`	A logical value specifying whether the result should be simplified to a vector or matrix if possible.

Details

Subsets of x can be specified either via the by argument or via the start, end, width, frequency, and delta arguments.

For example, if start and end are specified, then:

aggregate(x, FUN=FUN, start=start, end=end, ..., simplify=simplify)

is equivalent to:

sapply(seq_along(start),
         function(i) FUN(x[start[i]:end[i]], ...), simplify=simplify)

(replace x[start[i]:end[i]] with 2D-style subsetting x[start[i]:end[i], ] if x is a DataFrame object).

Examples

x <- Rle(10:2, 1:9)
aggregate(x, x > 4, mean)
aggregate(x, FUN=mean, start=1:26, width=20)

## Note that aggregate() works on a DataFrame object the same way it
## works on an ordinary data frame:
aggregate(DataFrame(state.x77), list(Region=state.region), mean)
aggregate(weight ~ feed, data=DataFrame(chickwts), mean)

library(IRanges)
by <- IRanges(start=1:26, width=20, names=LETTERS)
aggregate(x, by, is.unsorted)

S4Vectors

Foundation of vector-like and list-like containers in Bioconductor

v0.28.1

Artistic-2.0

Authors

H. Pagès, M. Lawrence and P. Aboyoun

Initial release

aggregate-methods

Description

Usage

Arguments

Details

See Also

Examples

S4Vectors

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