[BioC] Examples outdated in "Bioinformatics and Computational Biology Solutions Using R and Bioconductor"

[Peng Yu]

Hi,

I still run into other problems with the following fixes. Can some
more experienced BioC user help update these files and post them on
BioC website? All new users will appreciate your help!

Regards,
Peng

On Sun, Aug 9, 2009 at 7:30 AM, Heidi Dvinge<heidi at ebi.ac.uk> wrote:
> Hello Peng,
>
> please keep discussions to the list, so that other people can chime in as
> well.
>
> I'm not familiar with the details of xtable, but in the example you link
> to below it seems like the function xtable.matrix() does exist, but it's
> not exported by the name space. However, simply using xtable() works fine
> for me, and gives the same result at calling xtable.matrix() specifically
> (code shown below).
>
> There might be an updated version of the examples from "Bioinformatics and
> Computational Biology Solutions Using R and Bioconductor" somewhere;
> someone else can probably tell you. My best advice though is, that when
> something doesn't work, simply do a search for that function/package ;)
> Typing ?xtable.matrix gives you the xtable help page, which a.o. says "The
> available method functions for xtable are given by methods(xtable)."
>
> Regards
> \Heidi
>
>> library(GO.db)
>> library(xtable)
>> methods(xtable)
>  [1] xtable.anova*           xtable.aov*             xtable.aovlist*
>  xtable.coxph*
>  [5] xtable.data.frame*      xtable.glm*             xtable.lm*
>  xtable.matrix*
>  [9] xtable.prcomp*          xtable.summary.aov*
> xtable.summary.aovlist* xtable.summary.glm*
> [13] xtable.summary.lm*      xtable.summary.prcomp*  xtable.table*
>  xtable.ts*
> [17] xtable.zoo*
>
>   Non-visible functions are asterisked
>>  goTerms <- contents(GOTERM)
>> goCats <- sapply(goTerms, Ontology)
>>  gCnums <- table(goCats)[c("BP","CC", "MF")]
>> gCmat <- matrix(as.integer(gCnums), dimnames=list(c("BP","CC","MF"),
> "Number of terms"))
>>  xtable.matrix(gCmat, display=c("d","d"), caption="Number of GO terms
> per ontology.", label="ta:GOprops")
> Error: could not find function "xtable.matrix"
>> xtable:::xtable.matrix(gCmat, display=c("d","d"), caption="Number of GO
> terms per ontology.", label="ta:GOprops")
> % latex table generated in R 2.9.0 by xtable 1.5-5 package
> % Sun Aug  9 13:17:48 2009
> \begin{table}[ht]
> \begin{center}
> \begin{tabular}{rr}
>  \hline
>  & Number of terms \\
>  \hline
> BP & 16067 \\
>  CC & 2297 \\
>  MF & 8506 \\
>   \hline
> \end{tabular}
> \caption{Number of GO terms per ontology.}
> \label{ta:GOprops}
> \end{center}
> \end{table}
>> xtable(gCmat, display=c("d","d"), caption="Number of GO terms per
> ontology.", label="ta:GOprops")
> % latex table generated in R 2.9.0 by xtable 1.5-5 package
> % Sun Aug  9 13:17:59 2009
> \begin{table}[ht]
> \begin{center}
> \begin{tabular}{rr}
>  \hline
>  & Number of terms \\
>  \hline
> BP & 16067 \\
>  CC & 2297 \\
>  MF & 8506 \\
>   \hline
> \end{tabular}
> \caption{Number of GO terms per ontology.}
> \label{ta:GOprops}
> \end{center}
> \end{table}
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xtable_1.5-5        GO.db_2.2.11        RSQLite_0.7-1       DBI_0.2-4
>         AnnotationDbi_1.6.0
> [6] Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.0
>
>
>
>
>> Hi Heidi,
>>
>> I have figured out how to change the package names. But there are
>> still some command that is not running, for example 'xtable.matrix' in
>> the script that I pointed out in my orginal post.
>>
>> Could you please take a look how to correct these commands?
>>
>> Regards,
>> Peng
>>
>> On Sun, Aug 9, 2009 at 2:58 AM, Heidi Dvinge<heidi at ebi.ac.uk> wrote:
>>> Hi Peng,
>>>
>>> in general, all the annotation package now have an ".db" ending to
>>> reflect
>>> an underlying change to a database structure. In this particular case
>>> you'd therefore want GO.db, but the same would apply to e.g. KEGG.db,
>>> and
>>> all the chip annotation packages (moe430a.db, hgu133a.db,
>>> mogene10stprobeset.db etc.).
>>>
>>> Please see
>>> http://www.bioconductor.org/packages/release/AnnotationData.html for all
>>> the annotation packages.
>>>
>>> Best
>>> \Heidi
>>>
>>>
>>>> Hi,
>>>>
>>>> The examples in "Bioinformatics and Computational Biology Solutions
>>>> Using R and Bioconductor" are outdated. For example, I don't find the
>>>> package "GO" in
>>>> http://www.bioconductor.org/mogr/chapter-code/metaOverview.R
>>>>
>>>> I'm wondering if somebody can help updated the examples to reflect the
>>>> changes in BioC in the last 4 years.
>>>>
>>>> Regards,
>>>> Peng
>>>>
>>>> _______________________________________________
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>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>>
>>>
>>
>
>
>