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rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
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Method for gene-gene correlations #28

Open Yale73 opened 3 years ago

Yale73 commented 3 years ago

Hi iCellR,

Thanks for the great cell-cell correlation function. Do you mind tell me which method we used for the correlation analysis, eg Pearson, Spearman, etc? Also, we don't quite understand why

if (PVal == 0) {
        PVal = "2.2e-16"
    }

Is it the reason our PVal is very small?

thanks, Yale

rezakj commented 3 years ago

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

Yale73 commented 3 years ago

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