I wrote my previous message too quickly. Apologies.

Your functions must have the signature

function(df, object, ...)

df is current data.frame represenation of the object,
object is the *original* object (so that the class can be identified),
... are passed in from the call to publish

And you can just place the generic modifyReportDF function at the beginning
of the list, rather than using getMethod. The getMethod thing I said is for
when you want to apply the default handling for a *different* class to your
object. It is a rare use-case, but came up recently so it was on my mind.

That will teach me to respond quickly to emails early in the morning.

Sorry about that.

~G


On Thu, Apr 24, 2014 at 7:18 AM, Gabriel Becker <gmbecker@ucdavis.edu>wrote:

> Assa,
>
> In general yes, if you want to add to the table you will be working with
> the data.frame.
>
> You can do so after the initial conversion, though, so you don't have to
> recreate the wheel to get from your object to an initial data.frame.
>
> To modify the default table (data.frame) generated for an object, you can
> pass publish()'s  .modifyDF parameter a function of list of functions, each
> of which should accept object (the data.frame) and "..." and return a
> data.frame.
>
> These will be called in order, each accepting the output from the last.
> The output of the final function is what will be transformed into HTML and
> inserted into the report.
>
> You'll probably want to add the default handling of your object type,
> which you can do by putting
> getMethod("modifyReportDF", "<your object's class>") at the beginning of
> the list.
>
> See section 4 of the ReportingTools basics vignette for example code.
>
> HTH,
> ~G
>
>
> On Thu, Apr 24, 2014 at 6:54 AM, Assa Yeroslaviz <frymor@gmail.com> wrote:
>
>> Thanks Jim,
>>
>> I have found in one of the forums a response from Jason (thanks again) for
>> the option to set annotation.db=NULL and though force the publish command
>> to work with the Ids I provide in the DESeqDataSet object.
>>
>> So this is now working, But I would like to have also the option to add
>> some annotations to the table.
>>
>> Is this only possible when working directly with a data .frame?
>>
>> Thanks again
>> Assa
>>
>> On Thu, Apr 24, 2014 at 3:45 PM, James W. MacDonald <jmacdon@uw.edu>
>> wrote:
>>
>> > Hi Assa,
>> >
>> > There may well be a way to work with Ensembl IDs, and you will likely
>> get
>> > an answer to your direct question from one of the maintainers.
>> >
>> > However you should note that ReportingTools simply takes the input
>> object
>> > and then coerces the data to a data.frame, which is then used to create
>> the
>> > HTML table. You can always create the data.frame to your own liking up
>> > front, and then pass that to publish(). While this is more work than
>> just
>> > passing in the DESeqDataSet, you do have complete control over the
>> output.
>> >
>> > Best,
>> >
>> > Jim
>> >
>> >
>> >
>> > On 4/24/2014 8:50 AM, Assa Yeroslaviz wrote:
>> >
>> >> Hi,
>> >>
>> >> Is it neccessary to have entrez gene IDs to work with this package?
>> >>
>> >> I am working on a dataset with Ensembl IDs. Do I need to convert them
>> to
>> >> Entrez?
>> >>
>> >> When trying to create a report for a DESeqDataSet or DESeqResults
>> objects
>> >> i
>> >> am getting the error messege:
>> >>
>> >> Error: Ids do not appear to be Entrez Ids for the specified species.
>> >>
>> >> Is there a way to work straight with the ensembl IDs?
>> >>
>> >> Thanks
>> >>
>> >> Assa
>> >>
>> >> my script:
>> >>
>> >> head(Counts_set)
>> >>                     A_pKO_aV_FCS G_pKO_aV_FCS M_pKO_aV_FCS D_pKO_aV
>> >> J_pKO_aV
>> >> ENSMUSG00000000001         4744         4632         4535     4748
>> >> 3736
>> >> ENSMUSG00000000003            0            0            0        0
>> >>  0
>> >> ENSMUSG00000000028         1246         1420         1429     2304
>> >> 1261
>> >> ENSMUSG00000000031            3           25           65        0
>> >> 50
>> >> ENSMUSG00000000037            0            0            0        0
>> >>  0
>> >> ENSMUSG00000000049            0            0            3        1
>> >>  3
>> >>
>> >> cds <- DESeqDataSetFromMatrix (
>> >>      countData =     Counts_set,
>> >>      colData   =     colData,
>> >>      design    = ~    condition
>> >>      )
>> >>
>> >> fit = DESeq(cds)
>> >> des2Report <- HTMLReport(shortName =paste('RNAseq_analysis_', group1,
>> "_",
>> >> group2, sep=""),title ='RNA-seq analysis of differential expression
>> using
>> >> DESeq2',reportDirectory = "./reports")
>> >> publish(fit,des2Report, pvalueCutoff=0.05,annotation.db="org.Mm.eg.db",
>> >> factor = colData(fit)$condition,reportDir="./reports")
>> >> Error: Ids do not appear to be Entrez Ids for the specified species.
>> >> finish(des2Report)
>> >>
>> >>
>> >>  sessionInfo()
>> >>>
>> >> R version 3.1.0 (2014-04-10)
>> >> Platform: x86_64-pc-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=en_US.UTF-8    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] parallel  stats     graphics  grDevices utils     datasets  methods
>> >> [8] base
>> >>
>> >> other attached packages:
>> >>   [1] org.Mm.eg.db_2.14.0     ReportingTools_2.4.0
>>  AnnotationDbi_1.26.0
>> >>   [4] Biobase_2.24.0          RSQLite_0.11.4          DBI_0.2-7
>> >>   [7] knitr_1.5               DESeq2_1.4.0
>> >>  RcppArmadillo_0.4.200.0
>> >> [10] Rcpp_0.11.1             GenomicRanges_1.16.2    GenomeInfoDb_1.0.2
>> >> [13] IRanges_1.22.3          BiocGenerics_0.10.0
>> >>
>> >> loaded via a namespace (and not attached):
>> >>   [1] annotate_1.42.0          AnnotationForge_1.6.0
>> >> BatchJobs_1.2
>> >>   [4] BBmisc_1.5               BiocParallel_0.6.0
>> >> biomaRt_2.20.0
>> >>   [7] Biostrings_2.32.0        biovizBase_1.12.0
>> >> bitops_1.0-6
>> >> [10] brew_1.0-6               BSgenome_1.32.0
>> >> Category_2.30.0
>> >> [13] cluster_1.14.4           codetools_0.2-8
>> >> colorspace_1.2-4
>> >> [16] dichromat_2.0-0          digest_0.6.4
>> >> edgeR_3.6.0
>> >> [19] evaluate_0.5.3           fail_1.2
>> >> foreach_1.4.2
>> >> [22] formatR_0.10             Formula_1.1-1
>> >> genefilter_1.46.0
>> >> [25] geneplotter_1.42.0       GenomicAlignments_1.0.0
>> >> GenomicFeatures_1.16.0
>> >> [28] ggbio_1.12.0             ggplot2_0.9.3.1
>> >> GO.db_2.14.0
>> >> [31] GOstats_2.30.0           graph_1.42.0
>> >> grid_3.1.0
>> >> [34] gridExtra_0.9.1          GSEABase_1.26.0
>> >> gtable_0.1.2
>> >> [37] Hmisc_3.14-4             hwriter_1.3
>> >> iterators_1.0.7
>> >> [40] lattice_0.20-24          latticeExtra_0.6-26
>> >> limma_3.20.1
>> >> [43] locfit_1.5-9.1           MASS_7.3-29
>> >> Matrix_1.1-2
>> >> [46] munsell_0.4.2            PFAM.db_2.14.0
>> >> plyr_1.8.1
>> >> [49] proto_0.3-10             RBGL_1.40.0
>> >> RColorBrewer_1.0-5
>> >> [52] RCurl_1.95-4.1           reshape2_1.2.2
>> >> R.methodsS3_1.6.1
>> >> [55] R.oo_1.18.0              Rsamtools_1.16.0
>> >> rtracklayer_1.24.0
>> >> [58] R.utils_1.29.8           scales_0.2.4
>> >> sendmailR_1.1-2
>> >> [61] splines_3.1.0            stats4_3.1.0
>> >> stringr_0.6.2
>> >> [64] survival_2.37-7          tools_3.1.0
>> >> VariantAnnotation_1.10.0
>> >> [67] XML_3.98-1.1             xtable_1.7-3
>> >> XVector_0.4.0
>> >> [70] zlibbioc_1.10.0
>> >>
>> >>         [[alternative HTML version deleted]]
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor@r-project.org
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives: http://news.gmane.org/gmane.
>> >> science.biology.informatics.conductor
>> >>
>> >
>> > --
>> > James W. MacDonald, M.S.
>> > Biostatistician
>> > University of Washington
>> > Environmental and Occupational Health Sciences
>> > 4225 Roosevelt Way NE, # 100
>> > Seattle WA 98105-6099
>> >
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
> --
> Gabriel Becker
> Graduate Student
> Statistics Department
> University of California, Davis
>



-- 
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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