Why is the pValue peaks very high in EpigenomeRoadMap data.

Question

[Fawzi Yassine]

Why is the pValue peaks very high in EpigenomeRoadMap data. Does that mean that the peaks are insignificant? For example: `> meanadult.brain.gr$pValue)

19.2`

Answer 1

[colin.kern]

A raw p-value is in the range 0 to 1, so 19.2 is clearly not a p-value. The narrowPeak and broadPeak formats, which are standard formats for peak calls that are extended from the BED format, represent p- and q-values as -log10 transformed values. The Roadmap data structure is probably derived from this format and uses the same conversion. So 19.2 is actually a p-value of 10^(-19.2).

[Fawzi Yassine]

Thanks, I didn't notice that. Do you know what is the difference between the narrowPeak and broadPeak formats?

[colin.kern]

You can see the format specifications here: https://genome.ucsc.edu/FAQ/FAQformat.html#format13

The only difference is the narrowPeak format has one additional column that indicates the peak summit.