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

[Deepayan Sarkar]

On Mon, Mar 23, 2009 at 11:18 AM,  <ig2ar-saf2 at yahoo.co.uk> wrote:
>
> 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")

Try

alignedLocs <- as(aln_chr1, "GenomeData")

(sorry for the confusing names, but somewhat inevitable for a devel package).

-Deepayan