adjust_proximalCPs {InPAS} | R Documentation |
adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq
adjust_proximalCPs( CPs, MINSIZE, PolyA_PWM, genome, classifier, classifier_cutoff, shift_range, search_point_START, step = 1 )
CPs |
the outputs of |
MINSIZE |
min size for short from |
PolyA_PWM |
PolyA position weight matrix |
genome |
a BSgenome::BSgenome object |
classifier |
cleanUpdTSeq classifier |
classifier_cutoff |
cutoff value of the classifier |
shift_range |
the searching range for the better CP sites |
search_point_START |
just in case there is no better CP sites |
step |
adjust step, default 1, means adjust by each base by cleanUpdTSeq. |
keep same as search_proximalCPs()
, which can be handled by
polish_CPs()
.
Jianhong Ou
search_proximalCPs()
, polish_CPs()
, adjust_proximalCPsByPWM()
,
adjust_proximalCPsByNBC()
, get_PAscore()
,get_PAscore2()