proximalAdj {InPAS} | R Documentation |
adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq
proximalAdj(CPs, MINSIZE, PolyA_PWM, genome, classifier, classifier_cutoff, shift_range, search_point_START, step=1)
CPs |
the outputs of searchProximalCPs |
MINSIZE |
min size for short from |
PolyA_PWM |
PolyA position weight metrix |
genome |
a BSgenome object |
classifier |
cleanUpdTSeq classifier |
classifier_cutoff |
cutoff value of the classiffier |
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 searchProximalCPs, which can be handled by polishCPs.
Jianhong Ou
searchProximalCPs
, polishCPs
,
proximalAdjByPWM
, proximalAdjByCleanUpdTSeq
,
PAscore
,PAscore2