Selection of ranges and columns

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 RangesList, 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 RangesList, the ranges of which become the ranges in the new BigWigSelection.

Author(s)

Michael Lawrence

Examples

  rl <- IRanges::RangesList(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())

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(rtracklayer)
Loading required package: GenomicRanges
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/rtracklayer/BigWigSelection-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BigWigSelection-class
> ### Title: Selection of ranges and columns
> ### Aliases: BigWigSelection-class BigWigSelection
> ###   coerce,RangesList,BigWigSelection-method
> ###   coerce,GenomicRanges,BigWigSelection-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>   rl <- IRanges::RangesList(chr1 = IRanges::IRanges(c(1, 5), c(3, 6)))
> 
>   BigWigSelection(rl)
An object of class "BigWigSelection"
Slot "ranges":
RangesList 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"

>   as(rl, "BigWigSelection") # same as above
An object of class "BigWigSelection"
Slot "ranges":
RangesList 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"

> 
>   # do not select the 'score' column
>   BigWigSelection(rl, character())
An object of class "BigWigSelection"
Slot "ranges":
RangesList 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)

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>