[R] formatting a list
Charles C. Berry
cberry at tajo.ucsd.edu
Mon Oct 22 20:41:36 CEST 2007
Tomas,
Are you using R-2.6.0 ??
Each method works for me producing as list of 7000 vectors.
The file I used to test this is created by:
for (i in 1:7000) cat( seq(from=i,by=1,length=19),"\n",
sep='\t',file="tmp.tab",append=TRUE)
The first line is:
> scan("tmp.tab",nlines=1)
Read 19 items
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
>
The last line is
> scan("tmp.tab",skip=6999,nlines=1)
Read 19 items
[1] 7000 7001 7002 7003 7004 7005 7006 7007 7008 7009 7010 7011 7012 7013
7014 7015 7016 7017 7018
>
and each method recapitulates this:
> dat[[1]]
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
> dat[[7000]]
[1] 7000 7001 7002 7003 7004 7005 7006 7007 7008 7009 7010 7011 7012 7013
7014 7015 7016 7017 7018
>
The second method threw lots of warnings because open connections
must be closed. Those could be eliminated by explicitly opening and
closing the connection. Before using the second method
closeAllconnections() was sometimes needed, but the error it reported
differs from the one you mention.
I am using
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 6.0
year 2007
month 10
day 03
svn rev 43063
language R
version.string R version 2.6.0 (2007-10-03)
>
Chuck
On Mon, 22 Oct 2007, Tomas Vaisar wrote:
> Hi Chuck,
>
> thanks for your responses. I did not ignore your suggestions - I did
> try them and they did not produce what I need.
>
> The first one produced table with the same format as a read.table would
> generate, not not a list of lists.
> Second one gave me an error after returning Read 19 items multiple times
> : Error in textConnection(x) : all connections are in use
> The last one gave me similar error on the first step - Error in
> file(con, "r") : all connections are in use
>
> However, your last suggestion to make list of lists seems that it
> works. I will have to test more.
>
> Cheers,
>
> Tomas
>
> Charles C. Berry wrote:
>>
>> Tomas,
>>
>> Three different ways to create a list of 7000 vectors from a file of
>> 7000 rows and 19 columns are given here:
>>
>> http://article.gmane.org/gmane.comp.lang.r.general/97032
>>
>> which I think is what you are asking for.
>>
>> If you truly need a list of 7000 lists each of length 1 containing a
>> vector of length 19, then do this:
>>
>> list.of.lists.of.one.vector.each <- lapply( list.of.vectors, list )
>>
>>
>> BTW, as this thread appears in
>>
>> http://news.gmane.org/gmane.comp.lang.r.general
>>
>> the above article was the firt reply to your original query. I am
>> puzzled as to why you did not simply implement one of the three
>> methods shown there.
>>
>> Chuck
>>
>> On Mon, 22 Oct 2007, Tomas Vaisar wrote:
>>
>>> Hi Jim,
>>>
>>> I really appreciate your help.
>>> From the input file I have - 19 columns, 7000 rows - the scan gives me
>>> the desired format of a list consisting of 19 lists with 7000 values
>>> each.
>>> However I need a list of 7000 lists with 19 values each. (e.g. each row
>>> of my input file should be a separate list bound in a list of all these
>>> lists)
>>> I use both commands you suggested -
>>> x <- scan('temp.txt', what=c(rep(list(0), 19)))
>>> followed by
>>> x.matrix <- do.call('rbind', x) # gives 7000 x 19 matrix.
>>>
>>> Although this makes a matrix of the correct dimensions it is not the
>>> "list of lists" the ROCR package expects as input. Can you convert this
>>> matrix into a "list of lists"? Or is there a simple way in R to convert
>>> a table into such a "list of lists"?
>>>
>>> Thanks again,
>>>
>>> Tomas
>>>
>>>
>>> jim holtman wrote:
>>>> That is what I thought and that is the format that the 'scan' approach
>>>> should provide. I was just confused when you said that you were going
>>>> to have to transpose it, write it and then read it back in for some
>>>> reason. I understand that Excel can not handle 7000 columns, but was
>>>> wondering where that came into play.
>>>>
>>>> On 10/21/07, Tomas Vaisar <tvaisar at u.washington.edu> wrote:
>>>>
>>>>> The data I have is tab delimited file with 7000 lines of 19 values
>>>>> each
>>>>> (representing 7000 permutations on 19 variables). I want to get it
>>>>> into
>>>>> the ROCR package which expects the data to be in lists - single
>>>>> list of
>>>>> 19 values for each permutation, e.g. list of 7000 lists of 19
>>>>> values each.
>>>>>
>>>>> I hope this is little clearer.
>>>>>
>>>>> Tomas
>>>>>
>>>>> jim holtman wrote:
>>>>>
>>>>>> What is it that you want to do? The 'scan' statement give you a list
>>>>>> of length 7000 with 19 entries each. Do you want to create a matrix
>>>>>> that has 7000 rows by 19 columns? If so, then you just have to take
>>>>>> the output of the 'scan' and do:
>>>>>>
>>>>>> x.matrix <- do.call('rbind', x) # gives 7000 x 19 matrix.
>>>>>>
>>>>>> So I am still not sure exactly what your input is and what you
>>>>>> want to
>>>>>> do with it.
>>>>>>
>>>>>> On 10/21/07, Tomas Vaisar <tvaisar at u.washington.edu> wrote:
>>>>>>
>>>>>>
>>>>>>> Hi Jim,
>>>>>>>
>>>>>>> thanks a lot. It works, however - my other problem is that I
>>>>>>> need to
>>>>>>> transpose the original table before reading it into the list
>>>>>>> because the
>>>>>>> data come from Excel and it can't handle 7000 columns. I could
>>>>>>> read it
>>>>>>> in R transpose end write into a new tab delim file and then read
>>>>>>> it back
>>>>>>> in, but I would think that there might be a way in R to do both.
>>>>>>> Would you know about the way?
>>>>>>>
>>>>>>> Tomas
>>>>>>>
>>>>>>> jim holtman wrote:
>>>>>>>
>>>>>>>
>>>>>>>> another choice is:
>>>>>>>>
>>>>>>>> x <- scan('temp.txt', what=c(rep(list(0), 19)))
>>>>>>>>
>>>>>>>> On 10/20/07, Tomas Vaisar <tvaisar at u.washington.edu> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I am new to R and need to read in a file with 19 columns and
>>>>>>>>> 7000 rows
>>>>>>>>> and make it into a list of 7000 lists with 19 items each. For a
>>>>>>>>> simpler case of 10 by 10 table I used x <-scan("file",
>>>>>>>>> list(0,0,0,0,0,0,0,0,0,0)), perhaps clumsy, but it did the job.
>>>>>>>>> However with the large 19x7000 (which needs to be transposed) I
>>>>>>>>> am not
>>>>>>>>> sure how to go about it.
>>>>>>>>>
>>>>>>>>> Coudl somebody suggest a way?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Tomas
>>>>>>>>>
>>>>>>>>> ______________________________________________
>>>>>>>>> R-help at r-project.org mailing list
>>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>>
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> 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.
>>>
>>
>> Charles C. Berry (858) 534-2098
>> Dept of Family/Preventive
>> Medicine
>> E mailto:cberry at tajo.ucsd.edu UC San Diego
>> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
>> 92093-0901
>>
>>
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>
Charles C. Berry (858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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