Hello everyone,

Could someone please provide a working example (or point me to a good resource) of how 'lambda local' (along with lambda BG, 1k , 5k and 10k) is calculated for peak calling in MACS?

λlocal=max (λBG, [λregion, λ1k], λ5k, λ10k)

Does 'max' here mean the upper limit, based on whichever of the variables λBG, λregion, λ1k, λ5k, λ10k is the highest and hence the p-value being calculated taking this 'max' value for λ? Is λlocal a product/average/sum of all the other λs?

I have been unsuccessful in trying to understand it by referring to the script and the tutorial given in the link below:

https://github.com/taoliu/MACS/wiki/Advanced:-Call-peaks-using-MACS2-subcommands#The_genome_background

Also, is the 'mfold' (10-30 fold enrichment) parameter estimated w.r.t lambda BG?

Thanks!