adjust_distalCPs: Adjust distal CP sites by the cleanUpdTSeq algorithm

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

Adjust distal CP sites by the cleanUpdTSeq algorithm

Description

Adjust distal CP sites by the cleanUpdTSeq algorithm

Usage

adjust_distalCPs(
  distalCPs,
  classifier,
  classifier_cutoff,
  shift_range,
  genome,
  seqname,
  step = 1
)

Arguments

distalCPs	the output of search_distalCPs()
classifier	An R object for Naive Bayes classifier model, like the one in the cleanUpdTSeq package.
classifier_cutoff	A numeric(1) vector. A cutoff of probability that a site is classified as true CP sites. The value should be between 0.5 and 1. Default, 0.8.
shift_range	An integer(1) vector, specifying a shift range for adjusting the proximal and distal CP sites. Default, 50. It determines the range flanking the candidate CP sites to search the most likely CP sites.
genome	a BSgenome::BSgenome object
seqname	A character(1) vector, specifying a chromososome/scaffold name
step	An integer (1) vector, specifying the step size used for adjusting the proximal or distal CP sites using the Naive Bayes classifier from the cleanUpdTSeq package. Default 1. It can be in the range of 1 to 5.

Author(s)

Jianhong Ou

See Also

search_proximalCPs(), get_PAscore2()

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.