[BioC] Examples outdated in "Bioinformatics and Computational Biology Solutions Using R and Bioconductor"
Martin Morgan
mtmorgan at fhcrc.org
Tue Aug 11 00:13:37 CEST 2009
Peng Yu wrote:
> 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!
To follow the book verbatim, use R version 2.4 and correctly installed
Bioconductor packages (i.e., appropriate for R 2.4, as provided by
biocLite()). For a more recent treatment of similar material see
http://bioconductor.org/pub/biocases/. For the problem below, see
?xtable and "An Introduction to R", for instance section 10.9 (hint:
invoke as xtable(gcMat, ...) but take the time to understand why this works.
Martin
>
> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> 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
>>>>>
>>>>
>>>>
>>
>>
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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