adjust_proximalCPs: Adjust the proximal CP sites

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

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()

jianhong/InPAS documentation built on Oct. 27, 2023, 2:13 p.m.