Cross correlation metric in ChIP-seq experiments
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Entering edit mode
18 months ago
Aryan ▴ 30

(I am unable to format math equations on Biostar, so you may refer to my StackExchange post here to see the equations rendered)

I found this explanation of cross-correlation metric in ChIP-seq.

Now, the definition of Pearson's correlation coefficient between two random variables $X$ and $Y$ is $$\rho_x = \frac{Cov(X,Y)}{\sigma_x\sigma_y}$$ where $Cov(X,Y) = \frac{1}{n}\sum(X-\mu_x)(Y-\mu_Y)$ and $\sigma_x = \sqrt{\frac{1}{n}\sum(X-\mu_x)^2}$ (similarly for $Y$).

Given this definition, I am not sure what is being computed when the above link says:

Strand cross-correlation is computed as the Pearson’s linear correlation between the minus strand and the plus strand, after shifting minus strand by k base pairs

Following my above notation, what would $X$ be? What would $Y$ be?

chip-seq • 284 views
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