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" <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
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
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and provide commented, minimal, self-contained, reproducible code.
