Method for gene-gene correlations about icellr HOT 2 OPEN

Hi Yale,

Thank you, yes! It's the general r "cor.test" function that by default takes "pearson". Thanks for reminding me, I will add the option to change methods in the future. It is a bit of a lazy coding but yes.
I think at the time I wanted to replace 0 with the smallest p value because for some reason R was converting them to 0. But I will look into it in the future. Generally they are also represented with 4 stars (****) for p < 0.00001. If you want the exact very small p number you can run the "cor.test" outside of the function on the imputed data.

Hope this helps :)

Reza

from icellr.

Hi Reza,

You are right, they always report 0 if it is very small. Your code seems to keep the real p-value, right? As I always get XXe-267 or XXe-578, etc.

Also, I compared Pearson and Spearman, it seems Spearman is more suitable for single-cell data, as it considers the ordinal variables. Then can you tell me why you set the default Pearson?

Thanks for any correction.

Best,
Yale

from icellr.