adjust_proximalCPsByNBC: adjust the proximal CP sites by using Naive Bayes classifier...

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

adjust the proximal CP sites by using Naive Bayes classifier from cleanUpdTSeq

Description

adjust the proximal CP sites by using Naive Bayes classifier from cleanUpdTSeq

Usage

adjust_proximalCPsByNBC(
  idx.list,
  cov_diff.list,
  seqnames,
  starts,
  strands,
  genome,
  classifier,
  classifier_cutoff,
  shift_range,
  search_point_START,
  step = 1
)

Arguments

idx.list	the offset of positions of CP sites
cov_diff.list	the MSE values
seqnames	a character(n) vector, the chromosome/scaffolds' names
starts	starts
strands	strands
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	adjusting step, default 1, means adjust by each base by cleanUpdTSeq.

Details

the step for calculating is 10, can not do every base base it is really very slow.

Value

the offset of positions of CP sites after filter

Author(s)

Jianhong Ou

See Also

adjust_proximalCPsByPWM(), get_PAscore2()

jianhong/InPAS documentation built on June 8, 2025, 2:05 a.m.