BigWigSelection-class: Selection of ranges and columns

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description

A BigWigSelection represents a query against a BigWig file, see import.bw. It is simply a RangedSelection that requires its colnames parameter to be "score", if non-empty, as that is the only column supported by BigWig.

Constructor

BigWigSelection(ranges = GRanges(), colnames = "score"): Constructs a BigWigSelection with the given ranges and colnames. ranges can be either something coercible to a IntegerRangesList, a character identifying a genome (see GenomicSelection), or a BigWigFile, in which case the ranges are derived from the bounds of its sequences.

Coercion

as(from, "BigWigSelection"): Coerces from to a BigWigSelection object. Typically, from is a GRanges or a IntegerRangesList, the ranges of which become the ranges in the new BigWigSelection.

Author(s)

Michael Lawrence

Examples

  rl <- IRangesList(chr1 = IRanges::IRanges(c(1, 5), c(3, 6)))

  BigWigSelection(rl)
  as(rl, "BigWigSelection") # same as above

  # do not select the 'score' column
  BigWigSelection(rl, character())

Example output

Loading required package: GenomicRanges
Loading required package: stats4
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':

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
An object of class "BigWigSelection"
Slot "ranges":
IRangesList of length 1
$chr1
IRanges object with 2 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]         1         3         3
  [2]         5         6         2


Slot "colnames":
[1] "score"

An object of class "BigWigSelection"
Slot "ranges":
IRangesList of length 1
$chr1
IRanges object with 2 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]         1         3         3
  [2]         5         6         2


Slot "colnames":
[1] "score"

An object of class "BigWigSelection"
Slot "ranges":
IRangesList of length 1
$chr1
IRanges object with 2 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]         1         3         3
  [2]         5         6         2


Slot "colnames":
character(0)

Warning message:
system call failed: Cannot allocate memory 

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.