[BioC] export Views of Rle in rtracklayer

[Jason Lu]

Hi list,

I have a question and would like to get your help.
What I would like to get is to show the read coverage in the exon
regions (only) in the ucsc genome browser. My question is how to
export the Views so I can load into ucsc browser.
Here is what I have:

#
>cvg = coverage(ranges(ss))
>cvg.view = Views(cvg,ranges(exon.gr))  # exon.gr is a GRanges
>cvg.view
Views on a 22109556-length Rle subject

views:
        start      end width
 [1] 22109317 22109688   372 [5 5 7 5 6 6 6 5 5 5 5 5 4 4 5 8 8 8 9 9 9 9 ...]
 [2] 22084156 22084276   121 [4 4 4 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 ...]
 [3] 22083039 22083195   157 [2 1 1 0 0 0 1 1 1 1 2 2 2 2 2 2 2 2 2 3 3 4 ...]
 [4] 22079485 22079612   128 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 ...]
 [5] 22079020 22079144   125 [6 6 6 6 7 7 7 7 7 7 7 7 7 7 6 6 6 6 6 6 5 4 ...]

I don't know how to modify this view such as adding chromosome info
and export this 'cvg.view' in rtracklayer.
Thanks in advance.
Jason

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] rtracklayer_1.14.3    RCurl_1.7-0           bitops_1.0-4.1
 [4] Rsamtools_1.6.2       Biostrings_2.22.0     GenomicFeatures_1.6.4
 [7] AnnotationDbi_1.16.4  Biobase_2.14.0        GenomicRanges_1.6.3
[10] IRanges_1.12.2        BiocInstaller_1.2.1

loaded via a namespace (and not attached):
[1] BSgenome_1.22.0 DBI_0.2-5       RSQLite_0.10.0  XML_3.4-3
[5] biomaRt_2.10.0  tools_2.14.0    zlibbioc_1.0.0
>