import-bigwig.R

library('GenomicRanges')
library('derfinderData')
library('rtracklayer')
library('devtools')

## Find some bigwigs
bw <- dir(system.file('extdata', 'A1C', package = 'derfinderData'), full.names = TRUE)

## Regions to import
gr <- GRanges(c('chr21', 'chr21'), IRanges(c(9481564, 9963234), width = 1000))

## Import one
( import(BigWigFile(bw[1]), selection = gr[1]) )
( import(BigWigFile(bw[1]), selection = gr[1], as = 'NumericList') )

## Now import with 2 ranges
( import(BigWigFile(bw[1]), selection = gr) )
( import(BigWigFile(bw[1]), selection = gr, as = 'NumericList') )
traceback()

## Session info
options(width = 100)
session_info()
Sys.time()

import-bigwig.txt

> library('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 object is masked from ‘package:stats’:

    xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
> library('derfinderData')
> library('rtracklayer')
> library('devtools')
>
> ## Find some bigwigs
> bw <- dir(system.file('extdata', 'A1C', package = 'derfinderData'), full.names = TRUE)
>
> ## Regions to import
> gr <- GRanges(c('chr21', 'chr21'), IRanges(c(9481564, 9963234), width = 1000))
>
> ## Import one
> ( import(BigWigFile(bw[1]), selection = gr[1]) )
GRanges object with 1 range and 1 metadata column:
      seqnames             ranges strand |              score
         <Rle>          <IRanges>  <Rle> |          <numeric>
  [1]    chr21 [9481565, 9481639]      * | 0.0299999993294477
  -------
  seqinfo: 1 sequence from an unspecified genome
> ( import(BigWigFile(bw[1]), selection = gr[1], as = 'NumericList') )
NumericList of length 1
[[1]] 0 0.0299999993294477 0.0299999993294477 0.0299999993294477 ... 0 0 0 0
>
> ## Now import with 2 ranges
> ( import(BigWigFile(bw[1]), selection = gr) )
GRanges object with 2 ranges and 1 metadata column:
      seqnames             ranges strand |              score
         <Rle>          <IRanges>  <Rle> |          <numeric>
  [1]    chr21 [9481565, 9481639]      * | 0.0299999993294477
  [2]    chr21 [9963234, 9963254]      * | 0.0700000002980232
  -------
  seqinfo: 1 sequence from an unspecified genome
> ( import(BigWigFile(bw[1]), selection = gr, as = 'NumericList') )
Error in .local(con, format, text, ...) :
  attempt to set index 1/1 in SET_VECTOR_ELT
> traceback()
4: .Call(BWGFile_query, path.expand(path(con)), as.list(which),
       identical(colnames(selection), "score"), as == "NumericList")
3: .local(con, format, text, ...)
2: import(BigWigFile(bw[1]), selection = gr, as = "NumericList")
1: import(BigWigFile(bw[1]), selection = gr, as = "NumericList")
>
> ## Session info
> options(width = 100)
> session_info()
Session info ---------------------------------------------------------------------------------------
 setting  value
 version  R version 3.2.0 Patched (2015-05-18 r68382)
 system   x86_64, darwin10.8.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 tz       America/Detroit

Packages -------------------------------------------------------------------------------------------
 package              * version  date       source
 Biobase                2.29.1   2015-05-03 Bioconductor
 BiocGenerics         * 0.15.0   2015-04-17 Bioconductor
 BiocParallel           1.3.12   2015-05-19 Bioconductor
 Biostrings             2.37.2   2015-05-07 Bioconductor
 bitops                 1.0-6    2013-08-17 CRAN (R 3.2.0)
 colorout             * 1.0-2    2015-05-19 local
 derfinderData        * 0.103.0  2015-05-19 Bioconductor
 devtools             * 1.8.0    2015-05-09 CRAN (R 3.2.0)
 digest                 0.6.8    2014-12-31 CRAN (R 3.2.0)
 futile.logger          1.4.1    2015-04-20 CRAN (R 3.2.0)
 futile.options         1.0.0    2010-04-06 CRAN (R 3.2.0)
 GenomeInfoDb         * 1.5.3    2015-05-13 Bioconductor
 GenomicAlignments      1.5.9    2015-05-13 Bioconductor
 GenomicRanges        * 1.21.12  2015-05-17 Bioconductor
 git2r                  0.10.1   2015-05-07 CRAN (R 3.2.0)
 IRanges              * 2.3.8    2015-05-02 Bioconductor
 lambda.r               1.1.7    2015-03-20 CRAN (R 3.2.0)
 memoise                0.2.1    2014-04-22 CRAN (R 3.2.0)
 RCurl                  1.95-4.6 2015-04-24 CRAN (R 3.2.0)
 Rsamtools              1.21.5   2015-05-17 Bioconductor
 rtracklayer          * 1.29.5   2015-05-01 Bioconductor
 rversions              1.0.0    2015-04-22 CRAN (R 3.2.0)
 S4Vectors            * 0.7.2    2015-05-01 Bioconductor
 SummarizedExperiment   0.1.5    2015-05-17 Bioconductor
 XML                    3.98-1.1 2013-06-20 CRAN (R 3.2.0)
 XVector                0.9.1    2015-04-30 Bioconductor
 zlibbioc               1.15.0   2015-04-17 Bioconductor
> Sys.time()
[1] "2015-05-19 14:48:58 EDT"
>