adjust_proximalCPs: Adjust the proximal CP sites

View source: R/15.adjust_proximalCPs.R

adjust_proximalCPsR Documentation

Adjust the proximal CP sites

Description

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.

Usage

adjust_proximalCPs(
  CPs,
  PolyA_PWM,
  genome,
  classifier,
  classifier_cutoff,
  shift_range,
  search_point_START,
  step = 1,
  DIST2ANNOAPAP = 1000
)

Arguments

CPs

the outputs of search_proximalCPs()

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.

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()


haibol2016/InPAS documentation built on March 30, 2022, 10:30 a.m.