R help - Jun 2006 - rcor.test keeping column names

I have been using the function rcor.test in the ltm package and have
been trying to use it for p-values of pairwise correlations using the
pearson correlation .  However when I call the p-values from the output
it gives me back a number index instead of the row names (I transposed
the columns and rows to compare genes and not columns) which shows up as

column.number column.number p-value  



Is there anyway to get out an output that looks like

column.name1 correlation p-value column.name2

for each pairwise comparison or at least to get

column.name1 column.name2 p.value



Damion Nero
Plant Molecular Biology Lab
Department of Biology 
New York University

you can try something like the following:

mat <- matrix(rnorm(1000), 100, 10, dimnames = list(NULL, 
LETTERS[1:10]))
rcts <- rcor.test(mat)
################
rcts

pvals <- as.data.frame(rcts$p.values)
pvals$corr <- rcts$cor.mat[lower.tri(rcts$cor.mat)]
pvals[1:2] <- sapply(pvals[1:2], factor, levels = 1:ncol(mat), labels 
= colnames(mat), simplify = FALSE)
pvals[c(1,2,4,3)]


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
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: "Damion Colin Nero" <dcn208 at nyu.edu>
To: <r-help at stat.math.ethz.ch>
Sent: Tuesday, June 20, 2006 2:49 PM
Subject: [R] rcor.test keeping column names

>I have been using the function rcor.test in the ltm package and have
> been trying to use it for p-values of pairwise correlations using 
> the
> pearson correlation .  However when I call the p-values from the 
> output
> it gives me back a number index instead of the row names (I 
> transposed
> the columns and rows to compare genes and not columns) which shows 
> up as
>
> column.number column.number p-value
>
>
>
> Is there anyway to get out an output that looks like
>
> column.name1 correlation p-value column.name2
>
> for each pairwise comparison or at least to get
>
> column.name1 column.name2 p.value
>
>
>
> Damion Nero
> Plant Molecular Biology Lab
> Department of Biology
> New York University
>
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