[R] Howto Compute Pairwise Similarity/Correlation Matrix from aData Frame

[Gundala Viswanath]

Dear Dimitris,

Thanks so much for the reply.

However I got this memory error,when
I run it on my data  (12.7Mb).

Is there a way I can make the
code more memory susceptible.

My dataset can be found here:
http://dpaste.com/57274/plain/

__BEGIN__
> data <- read.table("mydata.txt")
> nofsamp <- ncol(data)
> nofrow <- nrow(data)
>
> mat.data <- data.matrix(data)
> corr <- cor(t(mat.data))
R(1294) malloc: *** mmap(size=3948052480) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(1294) malloc: *** mmap(size=3948052480) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error: cannot allocate vector of size 3.7 Gb
Execution halted
__END__


- Gundala Viswanath
Jakarta - Indonesia


On Wed, Jun 18, 2008 at 4:39 PM, Dimitris Rizopoulos
<dimitris.rizopoulos at med.kuleuven.be> wrote:
> try this:
>
> mat.data <- data.matrix(data)
> cor(t(mat.data))
>
>
> I hope it helps.
>
> Best,
> Dimitris
>
> ----
> Dimitris Rizopoulos
> Biostatistical Centre
> School of Public Health
> Catholic University of Leuven
>
> Address: Kapucijnenvoer 35, Leuven, Belgium
> Tel: +32/(0)16/336899
> Fax: +32/(0)16/337015
> Web: http://med.kuleuven.be/biostat/
>    http://www.student.kuleuven.be/~m0390867/dimitris.htm
>
>
> ----- Original Message ----- From: "Gundala Viswanath" <gundalav at gmail.com>
> To: <r-help at stat.math.ethz.ch>
> Sent: Wednesday, June 18, 2008 8:55 AM
> Subject: [R] Howto Compute Pairwise Similarity/Correlation Matrix from aData
> Frame
>
>
>> Hi,
>>
>> I have the following 5 vectors. I wish to compute
>> the pairwise Pearson Correlation matrix with this data.frame.
>> Is there a compact way to do it?
>>
>> At the end I hope to create a heatmap out of this correlation matrix.
>>
>> __BEGIN__
>>>
>>> data <- read.table("mydata.txt")
>>> print(data)
>>
>>         V1      V2      V3      V4      V5      V6      V7      V8 V9
>> 1       42.3    53.2    76.4    78.8    83.6    91.3    92.2   105.8 109.6
>> 2        6.8     9.7    12.7    13.1    14.6    16.3    17.2    17.9 18.1
>> 3       10.6    21.5    34.4    38.2    38.8    50.0    60.7    64.0 64.3
>> 4      215.3   227.4   227.7   245.0   257.2   260.0   269.8   287.3 340.2
>> 5        4.1     4.2     4.6     6.4     6.8     6.9    16.9    17.6 23.3
>>
>> __END__
>>
>> Currently I am stuck in constructing the very matrix itself from
>> double loop.
>>
>> __BEGIN__
>> data <- read.table("GDS596_part1.txt")
>> nofrow <- nrow(data)
>>
>> for (rwx in 1:nofrow) {
>>  print(data[rwx,])
>>  for (rwy in 1:nofrow) {
>>     print(data[rwy,])
>>
>>      thecor <- cor(data[rwx,],data[rwy.], method="pearson")
>>      # not sure how to proceed from here.
>>  }
>>
>> }
>> __END__
>>
>> Please advice.
>>
>> - Gundala Viswanath
>> Jakarta - Indonesia
>>
>> ______________________________________________
>> 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.
>>
>
>
> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>
>