get_PAscore {InPAS} | R Documentation |
calculate the CP score by using PWM of polyadenylation signal
get_PAscore(seqname, pos, str, idx, PWM, genome, ups = 50, dws = 50)
seqname |
a character(n) vector, the chromosome/scaffold' name |
pos |
genomic positions |
str |
DNA strand |
idx |
offset position |
PWM |
An R object for a position weight matrix (PWM) for a hexamer polyadenylation signal (PAS), such as AAUAAA. |
genome |
an object of BSgenome::BSgenome |
ups |
the number of upstream bases for PAS search. |
dws |
the number of downstream bases for PAS search. |
A list containing offset positions after PA score-based filtering
Jianhong Ou