get_zScoreCutoff: Calculate local background cutoff value

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

Calculate local background cutoff value

Description

calculate local background z-score cutoff

Usage

get_zScoreCutoff(
  background,
  chr.introns,
  chr.totalCov,
  chr.utr3,
  seqname,
  z = 2
)

Arguments

background	A character(1) vector, indicating how background coverage is defined.
chr.introns	An object of GenomicRanges::GRanges for introns of a give chromosome/scaffold
chr.totalCov	total coverage for a given chromosome/scaffold, an output from get_totalCov() for a given chromosome/scaffold
chr.utr3	An object of GenomicRanges::GRanges, an element of the output of extract_UTR3Anno() for a given chromosome/scaffold
seqname	A character(1), the name of a chromosome/scaffold
z	Z score cutoff value

Value

A named numeric vector containing local background Z-score cutoff values. The names are GRanges's name for 3' UTRs.

Author(s)

Jianhong Ou, Haibo Liu

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