View source: R/15.adjust_proximalCPsByPWM.R
adjust_proximalCPsByPWM | R Documentation |
adjust the proximal CP sites by polyA Position Weight Matrix. It only need the PWM to get match in upstream or downstream shift_range nr.
adjust_proximalCPsByPWM( idx, PolyA_PWM, seqnames, starts, strands, genome, shift_range, search_point_START )
idx |
the offset of positions of CP sites |
PolyA_PWM |
polyA PWM |
seqnames |
a character(n) vector, the chromosome/scaffolds' names |
starts |
start position in the genome |
strands |
strands |
genome |
an BSgenome::BSgenome object |
shift_range |
the shift range of PWM hits |
search_point_START |
Not use |
the hits is searched by Biostrings::matchPWM()
and the cutoff is
70\
the offset of positions of CP sites after filter
Jianhong Ou
adjust_proximalCPsByNBC()
, get_PAscore()
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