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

From: Gundala Viswanath <gundalav_at_gmail.com>
Date: Wed, 18 Jun 2008 15:55:48 +0900


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.


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. Received on Wed 18 Jun 2008 - 08:35:56 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 18 Jun 2008 - 09:30:42 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive