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songw01 / MEGENA

Multiscale embedded gene co-expression network analysis
GNU General Public License v3.0
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calculate.correlation() is not working for the preparation of signed module network #23

Open MithilG opened 1 year ago

MithilG commented 1 year ago

Hi, I am having gene expression dataset that are strongly positive and negatively correlated with each other. I am using the function calculate.correlation() to obtain the bidirectional rho values. However, I am obtaining the absolute rho values in the output.

Following is the code I am using for correlation:

MEGENA::calculate.correlation(CTF_normalized_M, doPerm = 100, is.signed = TRUE)

But If I run the normal correlation function cor() on the same dataset it returns the R values with its direction (-/+).

I am not able to understand why MEGENA gives only absolute values, is there any way to circumvent it?

Any suggestions or comments on this issue will be deeply appreciated!

Thank you very much in advance!