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spearman correlation and p-value as a matrix

Wed, Feb 13, 2013 10:10 PM

Thank you all for the answers. I really need to learn a lot. 
Bu I also discover cor2m(x, y, trim = TRUE, alpha = 0.05)
in ecodist package, which gives an output file with significant correlations.

?zg?l

Yj>HI,

#ag data was created
bg<- as.matrix(read.table(text=" 
???? Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 
Gi20Jun11? 0.001217??????? 0 0.001217??????? 0 0.000000??????? 0??????? 0??????? 0 0.001217??????? 0??????? 0??????? 0??????? 0??????? 0 0.001217??????? 0 0.001217 
Gi40Jun11? 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0??????? 0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0 0.000000 
Gi425Jun11 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0??????? 0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0 0.000000 
Gi45Jun11? 0.000000??????? 0 0.000000??????? 0 0.001513??????? 0??????? 0??????? 0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0 0.000000 
Gi475Jun11 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0??????? 0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0 0.000000 
Gi50Jun11? 0.000000??????? 0 0.000000??????? 0 0.000000??????? 0??????? 0??????? 0 0.000000??????? 0??????? 0??????? 0??????? 0??????? 0 0.000000??????? 0 0.000000 
",sep="",header=TRUE,stringsAsFactors=F))
set.seed(128)
ag<- matrix(rnorm(30),nrow=6)
colnames(ag)<- paste("ag",1:5,sep="")
bg_ag<-expand.grid(colnames(bg),colnames(ag),stringsAsFactors=FALSE)
?attr(bg_ag,"out.attrs")<- NULL
?library(Hmisc)
#correlation
resr<-do.call(rbind,lapply(split(bg_ag,1:nrow(bg_ag)),function(x) {res<-rcorr(cbind(bg[,x[,1]],ag[,x[,2]]),type="spearman")$r; row.names(res)<- rep(paste(x[1],x[2],sep="_"),2);res}))
?head(resr)
#???????????????? [,1]????? [,2]
#Otu00022_ag1 1.0000000 0.1309307
#Otu00022_ag1 0.1309307 1.0000000
#Otu00029_ag1 1.0000000?????? NaN
#Otu00029_ag1?????? NaN 1.0000000
#Otu00039_ag1 1.0000000 0.1309307
#Otu00039_ag1 0.1309307 1.0000000

#p-values
resP<-do.call(rbind,lapply(split(bg_ag,1:nrow(bg_ag)),function(x) {res<-rcorr(cbind(bg[,x[,1]],ag[,x[,2]]),type="spearman")$P; row.names(res)<- rep(paste(x[1],x[2],sep="_"),2);res}))
? head(resP)
#????????????????? [,1]????? [,2]
#Otu00022_ag1??????? NA 0.8047262
#Otu00022_ag1 0.8047262??????? NA
#Otu00029_ag1??????? NA?????? NaN
#Otu00029_ag1?????? NaN??????? NA
#Otu00039_ag1??????? NA 0.8047262
#Otu00039_ag1 0.8047262??????? NA

#If you need only the values
indx<-row(resr)%%2!=1
?resPnew<-as.matrix(resP[indx[,1],1])
?resrnew<-as.matrix(resr[indx[,1],1])

head(resPnew)
#????????????????? [,1]
#Otu00022_ag1 0.8047262
#Otu00029_ag1?????? NaN
#Otu00039_ag1 0.8047262
#Otu00042_ag1?????? NaN
#Otu00101_ag1 0.1583024
#Otu00105_ag1?????? NaN

head(resrnew)
#?????????????????? [,1]
#Otu00022_ag1? 0.1309307
#Otu00029_ag1??????? NaN
#Otu00039_ag1? 0.1309307
#Otu00042_ag1??????? NaN
#Otu00101_ag1 -0.6546537
#Otu00105_ag1??????? NaN

A.K.




----- Original Message -----
From: Ozgul Inceoglu <Ozgul.Inceoglu at ulb.ac.be>
To: r-help at r-project.org
Cc: 
Sent: Wednesday, February 13, 2013 4:48 AM
Subject: [R] spearman correlation and p-value as a matrix

I have two data matrices that I want to make the correlation between each column from data1 and each column from data 2 and also calculate the p-value Matrices dont have the same size and I tried such a script.

bg <- read.table (file.choose(), header=T, row.names) 
bg 
Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 
Gi20Jun11 0.001217 0 0.001217 0 0.000000 0 0 0 0.001217 0 0 0 0 0 0.001217 0 0.001217 
Gi40Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 
Gi425Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 
Gi45Jun11 0.000000 0 0.000000 0 0.001513 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 
Gi475Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 
Gi50Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000

ag <- read.table (file.choose(), header=T, row.names) 

for (i in 1:(ncol(bg))) 
for (j in 1:(ncol(ag))) 
print(c(i,j))
final_matrix <- matrix(rep("0",ncol(bg)*ncol(ag)),ncol=ncol(bg),nrow=ncol(ag))

cor <- cor.test(as.vector(as.matrix(bg[,i])),as.vector(as.matrix(ag[,j])), method="spearman")

#but the output is not matrice with all the values but a single correlation value

data:? bg[, i] and ag[, j] 
t = 2.2992, df = 26, p-value = 0.02978
alternative hypothesis: true correlation is not equal to 0 
95 percent confidence interval:
0.04485289 0.67986803 
sample estimates:
? ? ? cor 
0.4110515 

# How I can creat an outfile with all the correlations and p-values?

Thank you very much!
?zg?l

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?zg?l Inceoglu, PhD.

Universit? Libre de Bruxelles
Ecology of Aquatic Systems 
Campus de la plaine CP221  
Boulevard du triomphe  
1050 Bruxelles Belgium

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Ozgul Inceoglu spearman correlation and p-value as a matrix Feb 13 arun spearman correlation and p-value as a matrix Feb 14