view-summarization-methods: Summarize views on a vector-like object with numeric values

In IRanges: Foundation of integer range manipulation in Bioconductor

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)

IRanges documentation built on Dec. 14, 2020, 2 a.m.