[Bioc-sig-seq] Coercing to "GenomicData"

[ig2ar-saf2 at yahoo.co.uk]

Hello everybody,

I am trying to somehow visualize how my reads overlap (or cover) mouse chr1. A simple concept.

I create a readAlign object like this

aln <- readAlign(sp, myfile, filter = blah)

fine.

Then I compute the coverage like this

cov <- coverage(aln, start=1)[[1]]

fine.

The problem arises when when I try to construct from the coverage:

> gd <- as(cov, "GenomicData")
Error in as(cov, "GenomicData") : 
  no method or default for coercing "Rle" to "GenomicData"


So, basically, I am following Michael's tutorial
http://www.bioconductor.org/workshops/2008/SeattleNov08/rtracklayer/rtracklayer.pdf

Can anybody give me a pointer to figure out why it does not work for me?

Thank you,

Ivan



> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-03-10 r48103) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
 [1] rtracklayer_1.3.9                  RCurl_0.94-1                      
 [3] org.Mm.eg.db_2.2.6                 RSQLite_0.7-1                     
 [5] DBI_0.2-4                          AnnotationDbi_1.5.18              
 [7] Biobase_2.3.10                     BSgenome.Mmusculus.UCSC.mm9_1.3.11
 [9] ShortRead_1.1.43                   lattice_0.17-20                   
[11] BSgenome_1.11.13                   Biostrings_2.11.40                
[13] IRanges_1.1.48                    

loaded via a namespace (and not attached):
[1] grid_2.9.0  hwriter_1.1 XML_2.3-0