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

View source: R/15.adjust_proximalCPsByNBC.R

adjust_proximalCPsByNBCR Documentation

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 Nov. 5, 2024, 7:45 a.m.