[BioC] error in coverting readaligned object to GenomeData

[Martin Morgan]

On 07/19/2011 01:02 AM, Andreia Fonseca wrote:
> Hi Martin,
>
> I got the instructions in the vignette of PICS library which I want to
> use get my peaks object. Can PICS handle a GRanges object?

Hi Andreia -- I guess I spoke too quickly; I didn't realize that PICS 
implemented a method to coerce from AlignedRead to GenomeData; I guess 
this is really in the PICS package maintainer's court, so I'll get out 
of the way and let Raphael reply. Martin

> Thanks
> Andreia
>
> On Mon, Jul 18, 2011 at 11:25 PM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
>     Hi Andreia --
>
>
>     On 07/18/2011 11:04 AM, Andreia Fonseca wrote:
>
>         Dear all,
>
>         I am newby in analysing chip-seq data and I am getting an error
>         in coverting
>         my readaligned object to a GenomeData object
>
>         the commands that I am using are:
>         library(ShortRead)
>         library(PICS)
>         library(ChIPpeakAnno)
>         library(snowfall)
>         exDir<-("/RAID/Paula_chip_seq___data/")
>
>         dataIP_JKA<-readAligned(__dirPath=exDir, type="Bowtie",
>         pattern="110402_SN365_B_s_2___seq_GQG-1")
>         dataIP_JKA<- as(dataIP_JKA, "GenomeData")
>
>         Error in as.list.default(from) :
>            no method for coercing this S4 class to a vector
>         In addition: Warning message:
>         Storing reads only by their start positions is deprecated.
>         Please use a
>         range representation like GRanges.
>
>
>     I'm not sure where you're getting the instructions to coerce to a
>     'GenomicData' object, but these are no longer supported. For a
>     reproducible example, I ran
>
>       library(ShortRead)
>       example(readAligned)
>
>     and then
>
>       as(aln2, "GRanges")
>
>     But likely you'll want to (a) get Bowtie to export sam or bam files
>     and (b) use GenomicRanges::__readGappedAlignments to read the
>     aligned data. This will be a much smaller object, and already closer
>     to the format you're interested in.
>
>
>             dataCont_JKA
>
>         class: AlignedRead
>         length: 6443227 reads; width: 50 cycles
>         chromosome: chr20 chr17 ... chr8 chr21
>         position: 41162388 77764636 ... 59583233 34102674
>         strand: - - ... - +
>         alignQuality: NumericQuality
>         alignData varLabels: similar mismatch
>
>
>         I  am getting also an error when trying to convert the map file
>         into a
>         RangeData object
>
>         map<-read.table("/RAID/Paula___chip_seq_data/hg19.fa-50.bed",
>         header =
>         TRUE,colClasses = c("factor", "integer", "integer", "NULL"))
>
>             map<- as(map, "RangedData")
>
>
>     here I think you want to use rtracklayer::import().
>
>     Martin
>
>
>
>         thanks for the help.
>         Andreia
>
>
>
>         sessionInfo()
>         R version 2.13.1 (2011-07-08)
>         Platform: x86_64-unknown-linux-gnu (64-bit)
>
>         locale:
>           [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>           [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>           [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>           [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>           [9] LC_ADDRESS=C               LC_TELEPHONE=C
>         [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>         attached base packages:
>         [1] stats     graphics  grDevices utils     datasets  methods   base
>
>         other attached packages:
>           [1] snowfall_1.84                       snow_0.3-5
>           [3] ChIPpeakAnno_1.8.0                  limma_3.8.2
>           [5] org.Hs.eg.db_2.5.0                  GO.db_2.4.1
>           [7] RSQLite_0.9-1                       DBI_0.2-5
>           [9] AnnotationDbi_1.14.1
>           BSgenome.Ecoli.NCBI.20080805___1.3.17
>         [11] multtest_2.8.0                      Biobase_2.12.2
>         [13] biomaRt_2.8.1                       PICS_1.6.0
>         [15] BSgenome_1.20.0                     ShortRead_1.10.4
>         [17] Rsamtools_1.4.2                     lattice_0.19-30
>         [19] Biostrings_2.20.1                   GenomicRanges_1.4.6
>         [21] IRanges_1.10.4
>
>         loaded via a namespace (and not attached):
>         [1] grid_2.13.1     hwriter_1.2     MASS_7.3-13     RCurl_1.4-2
>         [5] splines_2.13.1  survival_2.36-9 XML_3.1-0
>
>
>
>
>
>
>
>     --
>     Computational Biology
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
>     Location: M1-B861
>     Telephone: 206 667-2793
>
>
>
>
> --
> ---------------------------------------------------------------------------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral at fm.ul.pt <mailto:email%3Aandreiaamaral at fm.ul.pt> ;
> andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793