this function expects a PWM which is based on information content transformation of a PPM. However, PWM can be more general than an IC matrix. Also, the trim_thresh is determined by multiplying input trim_threshold with max summed weights per position. In some cases, such as trimming a PPM, an absolute threshold may be desired. Potentially can be remedied by adding a boolean flag to control relative thresholding or not.
gReLU/src/grelu/interpret/motifs.py
Line 75 in 2760abd
this function expects a PWM which is based on information content transformation of a PPM. However, PWM can be more general than an IC matrix. Also, the
trim_threshis determined by multiplying inputtrim_thresholdwith max summed weights per position. In some cases, such as trimming a PPM, an absolute threshold may be desired. Potentially can be remedied by adding a boolean flag to control relative thresholding or not.