[R] write merged data frame to a file

[Andrea Franceschini]

Very Sorry for the instinctive bad comment...  I didn't express
correctly what I meant.
I meant that I would have never expected such behaviour, by default
(but may be I am wrong and most of the people need quoting, and hence
has sense to put it by default)

Problem solved,
Philipp guessed right.
It was just a quoting problem on the gene description.
The problem could be solved simply adding the (quote="") parameter to
the read.table command.

The quoting problem reversed into that strange behavior when I merged
two table (I don't know why).

Thankyou very much for the assistance,
Now that I realized that the quoting exists I can enjoying using R
(that as a tool perfectly suits my needs at the moment).

Have a nice day,
Andrea



On Mon, Jul 18, 2011 at 7:36 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>
> On Jul 18, 2011, at 11:10 AM, Andrea Franceschini wrote:
>
>> Dear Philipp,
>>
>>
>> You were right,
>> thankyou very much.
>> Effectively the second read.table didn't work (probably because of the
>> strange characters).
>>>
>>> From my point of view this is a very bad R bug.
>
> When I read this I thought it was an example of a young person just starting
> their education exhibiting Piaget's "preoperational" stage when applied to
> the task of learning a computer language.
>
> "the child begins to use symbols to represent objects. Early in this stage
> he also personifies objects. [snipped]  His thinking is influenced by
> fantasy -- the way he'd like things to be -- and he assumes that others see
> situations from his viewpoint."
>
> [Copied from a webpage for grade school teachers:
> http://www2.honolulu.hawaii.edu/facdev/guidebk/teachtip/piaget.htm ]
>
> But when I do a search in PubMed, I find that you may be an established
> researcher, so I thing the onus is now on you to demonstrate how R's
> behavior is different than the documented design goals for the read.table
> function.
>
>> I precisely inserted the "\t" separator in the read table command,
>> hence I would expect that everything is working.
>> How can I make it work ???
>
> I thought Pagel already gave you the answer, but your response is too
> general to be sure. What exactly did you find and can you provide a minimal
> code and data example that illustrates how read.table is acting in any way
> different than the documentation describes?
>
> --
> David.
>
>
>> Effectively there are several ' (i.e. apostrophe) characters in the
>> file. I guess are those that confuse R
>>
>>
>> Thankyou very much,
>> Best Regards,
>> Andrea
>>
>>
>>
>>
>> On Mon, Jul 18, 2011 at 4:32 PM, Philipp Pagel <p.pagel at wzw.tum.de> wrote:
>>>
>>> On Mon, Jul 18, 2011 at 04:00:29PM +0200, Andrea Franceschini wrote:
>>>>
>>>> I use version 13 of R in OSX (downloaded and installed less than 1 year
>>>> ago).
>>>
>>> Probably 2.13 ...
>>>
>>> [...] code omitted
>>>
>>>> The first lines are OK (i.e. 14 columns, like the dataframe), while at
>>>> a certain point I get lines with only 3 columns !!!
>>>> The bad lines that contain only 3 columns have the name and the
>>>> description of the gene (i.e. the content of the file that I merged
>>>> with).
>>>> Besides, these strange lines also get repeated (see the bottom).
>>>
>>> I havent't carefully analyzed your code so I may be wrong but my guess
>>> for
>>> all "weird behaviour of gene related data.frames" problems is this:
>>>
>>> Gene descriptions love to contain things like "Foo 5' obfuscation
>>> factor".  Note the "'" in the description which read.table will
>>> happily interpret as a quotation mark and eat lots of rows until it
>>> happens to encouter a closing counterpart. This leads to all kinds of
>>> funny results. So I bet your problem is not in write.table but in
>>> reading the data. Have a closer look at your data frame: are you
>>> really getting the expected number of observations in the merged
>>> data.frame? Are the rows in question really ok in the data frame? If
>>> my guess is correct you should be able to fix your problem by
>>> including quote="" in both your read.table commands.
>>>
>>> If it doesn't, also try comment.char="" - another popular source of
>>> problems.
>>>
>>> cu
>>>       Philipp
>>>
>>> --
>>> Dr. Philipp Pagel
>>> Lehrstuhl für Genomorientierte Bioinformatik
>>> Technische Universität München
>>> Wissenschaftszentrum Weihenstephan
>>> 85350 Freising, Germany
>>> http://webclu.bio.wzw.tum.de/~pagel/
>>>
>>
>> ______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius, MD
> West Hartford, CT
>
>