Hi Herve', I am having some issues with matchPWM, it works fine if I use it as described in the reference manual matchPWM(pwm1, Mmusculus) although if I try to wrap it in the bsapply function, I get an error message of the kind: > bsapply(params, pwm1) Error in function (classes, fdef, mtable) : unable to find an inherited method for function ‘matchPWM’ for signature ‘"matrix"’ Is bsapply designed to be used with matchPWM? I would like to use it with bsapply because I want to do it for all the sequences of the genome and mask some parts of the chromosomes corresponding to "peak calling regions" (using the option userMask) Thank you for your time, any suggestion would be very helpful. Best, Massimo [[alternative HTML version deleted]]