view-summarization-methods {IRanges} | R Documentation

## Summarize views on a vector-like object with numeric values

### Description

`viewApply` applies a function on each view of a Views or ViewsList object.

`viewMins`, `viewMaxs`, `viewSums`, `viewMeans` calculate respectively the minima, maxima, sums, and means of the views in a Views or ViewsList object.

### Usage

    viewApply(X, FUN, ..., simplify = TRUE)

    viewMins(x, na.rm=FALSE)
    ## S4 method for signature 'Views'
    min(x, ..., na.rm = FALSE)

    viewMaxs(x, na.rm=FALSE)
    ## S4 method for signature 'Views'
    max(x, ..., na.rm = FALSE)

    viewSums(x, na.rm=FALSE)
    ## S4 method for signature 'Views'
    sum(x, ..., na.rm = FALSE)

    viewMeans(x, na.rm=FALSE)
    ## S4 method for signature 'Views'
    mean(x, ...)

    viewWhichMins(x, na.rm=FALSE)
    ## S4 method for signature 'Views'
    which.min(x)

    viewWhichMaxs(x, na.rm=FALSE)
    ## S4 method for signature 'Views'
    which.max(x)

    viewRangeMins(x, na.rm=FALSE)

    viewRangeMaxs(x, na.rm=FALSE)

### Arguments

`X` | A Views object.
`FUN` | The function to be applied to each view in `X`.
`...` | Additional arguments to be passed on.
`simplify` | A logical value specifying whether or not the result should be simplified to a vector or matrix if possible.
`x` | An RleViews or RleViewsList object.
`na.rm` | Logical indicating whether or not to include missing values in the results.

### Details

The `viewMins`, `viewMaxs`, `viewSums`, and `viewMeans` functions provide efficient methods for calculating the specified numeric summary by performing the looping in compiled code.

The `viewWhichMins`, `viewWhichMaxs`, `viewRangeMins`, and `viewRangeMaxs` functions provide efficient methods for finding the locations of the minima and maxima.

### Value

For all the functions in this man page (except `viewRangeMins` and `viewRangeMaxs`): A numeric vector of the length of `x` if `x` is an RleViews object, or a List object of the length of `x` if it's an RleViewsList object.

For `viewRangeMins` and `viewRangeMaxs`: An IRanges object if `x` is an RleViews object, or an IRangesList object if it's an RleViewsList object.

### Note

For convenience, methods for `min`, `max`, `sum`, `mean`, `which.min` and `which.max` are provided as wrappers around the corresponding `view*` functions (which might be deprecated at some point).

### Author(s)

P. Aboyoun

### See Also

- The `slice` function for slicing an Rle or RleList object.

- view-summarization-methods in the XVector package for more view summarization methods.

- The RleViews and RleViewsList classes.

- The `which.min` and `colSums` functions.

### Examples

    ## Views derived from coverage
    x <- IRanges(start=c(1L, 9L, 4L, 1L, 5L, 10L),
                 width=c(5L, 6L, 3L, 4L, 3L,  3L))
    cvg <- coverage(x)
    cvg_views <- slice(cvg, lower=2)

    viewApply(cvg_views, diff)

    viewMins(cvg_views)
    viewMaxs(cvg_views)

    viewSums(cvg_views)
    viewMeans(cvg_views)

    viewWhichMins(cvg_views)
    viewWhichMaxs(cvg_views)

    viewRangeMins(cvg_views)
    viewRangeMaxs(cvg_views)

[Package IRanges version 2.14.12 Index]