View source: R/15.adjust_proximalCPs.R
adjust_proximalCPs | R Documentation |
Adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq. A few candidate sites, which are ranked by MSE from low to high, are used as input for adjusting. The final sites are the one with best score as PA sites, which are not necessary from the lowest MSE sites.
adjust_proximalCPs( CPs, PolyA_PWM, genome, classifier, classifier_cutoff, shift_range, search_point_START, step = 1, DIST2ANNOAPAP = 1000 )
CPs |
the outputs of |
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 |
An integer, specifying an adjusting step, default 1, means adjusting by each base by cleanUpdTSeq. |
DIST2ANNOAPAP |
An integer, specifying a cutoff for annotate MSE valleys with known proximal APAs in a given downstream distance. Default is 1500. |
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()
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