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

From: Dimitris Rizopoulos <dimitris.rizopoulos_at_med.kuleuven.be>
Date: Wed, 18 Jun 2008 09:39:54 +0200

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


> 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
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>

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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. Received on Wed 18 Jun 2008 - 07:43:10 GMT

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