Deleted:how find high correlated variables with a specific cutoff in R?
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12 months ago
sata72 • 0

I have a list of genes with two parameters for each genes. I want to create table with "Pearson" correlation and p value. this is a example of the list and the numbers are random selected.

I want to perform a correlation analysis between meth (col1) and exp (col2) to find highly correlated and statistically significant genes.

Input:

list    meth1   meth2   meth3   meth4   meth5   meth6   meth7   meth8   meth9   meth10  exp1    exp2    exp3    exp4    exp5    exp6    exp7    exp8    exp9    exp10
gene 1  1   1   1   1   1   1   1   1   1   1   7.2 7.2 7.2 7.2 7.2 7.2 7.2 7.2 7.2 7.2
gene 2  0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5
gene 3  0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 5   5   5   5   5   5   5   5   5   5
gene 4  0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 4   4   4   4   4   4   4   4   4   4
gene 5  0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 3   3   3   3   3   3   3   3   3   3
gene 6  0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 2   2   2   2   2   2   2   2   2   2
..
..

Expected output:

list    meth1   meth2   meth3   meth4   meth5   meth6   meth7   meth8   meth9   meth10  exp1    exp2    exp3    exp4    exp5    exp6    exp7    exp8    exp9    exp10   Correlation value  Pvalue 
gene 1  1   1   1   1   1   1   1   1   1   1   7.2 7.2 7.2 7.2 7.2 7.2 7.2 7.2 7.2 7.2   0.3  0.05
gene 2  0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5 7.5   0.8  0.04
gene 3  0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 5   5   5   5   5   5   5   5   5   5     0.9  0.06
gene 4  0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 4   4   4   4   4   4   4   4   4   4     0.2  0.01
gene 5  0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 3   3   3   3   3   3   3   3   3   3    -0.4  0.002
gene 6  0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 2   2   2   2   2   2   2   2   2   2     0.2  0.05
..
..
Pearson-correlation r • 684 views
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