slice-methods: Slice a vector-like or list-like object

In IRanges: Foundation of integer range manipulation in Bioconductor

Description

slice is a generic function that creates views on a vector-like or list-like object that contain the elements that are within the specified bounds.

Usage

slice(x, lower=-Inf, upper=Inf, ...)

## S4 method for signature 'Rle'
slice(x, lower=-Inf, upper=Inf,
      includeLower=TRUE, includeUpper=TRUE, rangesOnly=FALSE)

## S4 method for signature 'RleList'
slice(x, lower=-Inf, upper=Inf,
      includeLower=TRUE, includeUpper=TRUE, rangesOnly=FALSE)

Arguments

x	An Rle or RleList object, or any object coercible to an Rle object.
lower, upper	The lower and upper bounds for the slice.
includeLower, includeUpper	Logical indicating whether or not the specified boundary is open or closed.
rangesOnly	A logical indicating whether or not to drop the original data from the output.
...	Additional arguments to be passed to specific methods.

Details

slice is useful for finding areas of absolute maxima (peaks), absolute minima (troughs), or fluctuations within specified limits. One or more view summarization methods can be used on the result of slice. See ?`link{view-summarization-methods}`

Value

The method for Rle objects returns an RleViews object if rangesOnly=FALSE or an IRanges object if rangesOnly=TRUE.

The method for RleList objects returns an RleViewsList object if rangesOnly=FALSE or an IRangesList object if rangesOnly=TRUE.

Author(s)

P. Aboyoun

See Also

• view-summarization-methods for summarizing the views returned by slice.

• slice-methods in the XVector package for more slice methods.

• coverage for computing the coverage across a set of ranges.

• The Rle, RleList, RleViews, and RleViewsList classes.

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)
slice(cvg, lower=2)
slice(cvg, lower=2, rangesOnly=TRUE)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Views on a 14-length Rle subject

views:
    start end width
[1]     1   6     6 [2 2 2 3 3 2]
[2]    10  12     3 [2 2 2]
IRanges object with 2 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]         1         6         6
  [2]        10        12         3

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