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!
Özgül
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