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()


[Package InPAS version 2.1.0 Index]