Question: Peak annotation with HOMER. Statistics with the annStats parameter
gravatar for nanoide
10 months ago by
nanoide50 wrote:

Hi all. So I've been annotating some peaks with HOMER annotatePeaks. I have followed the instructions in the webpage for changing the TSS definition: Although HOMER doesn't allow you to explicitly change the definition of the region that is the TSS (-1kb to +100bp), you can "do it yourself" by sorting the annotation output in EXCEL by the "Distance to nearest TSS" column, and selecting those within the range you are interested in.

I have noticed that with the parameter annStats, HOMER can provide some statistics for an annotation enrichment analysis. I find these to be interesting, particularly the "Log2 Ratio (obs/exp)" for each annotation or the total size in bp. I have not found documentation on these stats. Of course these are not modified when I tune the TSS definition in Excel. Does anyone know how these are computed or how could I obtain these with other definitions for the promoter-TSS regions?


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