get_PAscore2: calculate the CP score

In haibol2016/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

calculate the CP score

Description

calculate CP score by cleanUpdTSeq

Usage

get_PAscore2(
  seqname,
  pos,
  str,
  idx,
  idx.gp,
  genome,
  classifier,
  classifier_cutoff
)

Arguments

seqname	a character(1) vector, the chromosome/scaffold's name
pos	genomic positions
str	DNA strand
idx	offset position
idx.gp	group number of the offset position
genome	an object of BSgenome::BSgenome
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.

Value

a data frame or NULL

Author(s)

Jianhong Ou, Haibo Liu

See Also

get_PAscore()

haibol2016/InPAS documentation built on Feb. 21, 2025, 6:26 p.m.