adjust_proximalCPs {InPAS}

R Documentation

adjust the proximal CP sites

Description

adjust the proximal CP sites by PolyA PWM and cleanUpdTSeq

Usage

adjust_proximalCPs(
  CPs,
  MINSIZE,
  PolyA_PWM,
  genome,
  classifier,
  classifier_cutoff,
  shift_range,
  search_point_START,
  step = 1
)

Arguments

CPs	the outputs of search_proximalCPs()
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.

Value

keep same as search_proximalCPs(), which can be handled by polish_CPs().

Author(s)

Jianhong Ou

See Also

search_proximalCPs(), polish_CPs(), adjust_proximalCPsByPWM(), adjust_proximalCPsByNBC(), get_PAscore(),get_PAscore2()

---