In the GreyListChIP manual, for the calcThreshold function, the p parameter is defined as 'The p-value threshold for marking bins as “grey”
The default value of that value is 0.99.

The general definition of p-value is the the probability of obtaining the test results (or test results that are at least as extreme as the ones obtained) under the assumption of the null hypothesis.

What is the null hypothesis for the statistical test that calcThreshold performs?

Hi,

The null hypothesis is that this region (typically a 1kb window) has about as many reads as you would get by chance if all the reads in this (input/control) sample were randomly distributed across the genome. The threshold is technically 1 - p... i.e. consider the region "grey" if there is less than a 0.01 chance that the accumulation of reads in this region is by chance. Yes, I'm a bit sloppy with my terminology sometimes... :)

It's not meant to be especially rigorous... I knocked together the package in a bit of a hurry.

Cheers,

• Gord