[Bioc-sig-seq] Reducing Solexa's export.txt in preparation for aChIP-seq analysis.

[ig2ar-saf2 at yahoo.co.uk]

Hello Deepayan and all,

I think that I understood well but the conversion does not work. This is a copy paste of the session:

library(ShortRead)
Loading required package: IRanges

Attaching package: 'IRanges'


    The following object(s) are masked from package:base :

     cbind,
     duplicated,
     order,
     pmax,
     pmax.int,
     pmin,
     pmin.int,
     rank,
     rbind,
     rep.int,
     sapply,
     sort,
     table,
     unique 

Loading required package: Biostrings
Loading required package: BSgenome
Loading required package: lattice
setwd('/scratch1/igregore/ChIPseq/runs/09-03-03/GERALD_16-03-2009_niddk/')
pattern <- "s_7_export.txt"
filt1 <- alignDataFilter(expression(filtering == "Y"))
filt2 <- chromosomeFilter("chr1.fa")
filt <- compose(filt1, filt2)
aln_chr1 <- readAligned(".", pattern, "SolexaExport", filter = filt)
class(aln_chr1)
[1] "AlignedRead"
attr(,"package")
[1] "ShortRead"
alignedLocs <- as(aln_chr1, "GenomicData")
Error in as(aln_chr1, "GenomicData") : 
  no method or default for coercing "AlignedRead" to "GenomicData"
alignedLocs <- as(aln_chr1, "RangedData")
Error in as(aln_chr1, "RangedData") : 
  no method or default for coercing "AlignedRead" to "RangedData"

I tried both GenomicData and RangedData because, I  understand, GenomicData does not exist anymore.

Can you give me any pointer to solve this?

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ShortRead_1.1.43   lattice_0.17-20    BSgenome_1.11.13   Biostrings_2.11.40
[5] IRanges_1.1.48    

loaded via a namespace (and not attached):
[1] Biobase_2.3.10 grid_2.9.0     hwriter_1.1    tools_2.9.0







----- Original Message ----
From: Deepayan Sarkar <deepayan.sarkar at gmail.com>
To: ig2ar-saf2 at yahoo.co.uk
Cc: bioc-sig-sequencing at r-project.org; Martin Morgan <mtmorgan at fhcrc.org>
Sent: Sunday, 22 March, 2009 10:30:34
Subject: Re: [Bioc-sig-seq] Reducing Solexa's export.txt in preparation for  aChIP-seq analysis.

On 3/19/09, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Hi Ivan --

[...]

>  chipseq is in the devel branch, and data structures there have not
>  been fully aligned with other established structures, and vice versa,
>  and the chipseq data structures are not fully described.  This is a
>  disconnect that we're working to resolve before the release.
>
>  Others might have something else to say.

You'll find these scripts more current:

http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/

The use of "AlignedList" has been superceded by the "GenomeData" and
"GenomeDataList" classes defined in the BSgenome package. You can
convert an "AlignedRead" object to a "GenomeData" object by

as(obj, "GenomeData")

(which basically strips off everything except alignment location). To
work with a list of "GenomeData" objects (e.g. different lanes), see
?GenomeDataList.

-Deepayan