searchDistalCPs: search distal CP sites

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Description

search distal CP sites

Usage

searchDistalCPs(chr.cov.merge, conn_next_utr3, 
            curr_UTR, window_size, 
            depth.weight, 
            long_coverage_threshold, 
            background, z2s)

Arguments

chr.cov.merge	coverage of current chromosome
conn_next_utr3	joint to next 3UTR or not (used for removeUTR3__UTR3)
curr_UTR	GRanges of current 3UTR
window_size	window size
depth.weight	output of depthWeight
long_coverage_threshold	cutoff value for coverage of long form 3UTR
background	local background range
z2s	cut off background scores. see zScoreThrethold

Value

a list

Author(s)

Jianhong Ou

See Also

distalAdj, PAscore2

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.