searchProximalCPs: search proximal CPsites

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

Description

search proximal CPsites

Usage

searchProximalCPs(CPs, curr_UTR, window_size, 
                MINSIZE, cutEnd, 
                search_point_START, 
                search_point_END,
                two_way=FALSE)

Arguments

CPs	output of searchDistalCPs or distalAdj
curr_UTR	GRanges of current 3UTR
window_size	window size
MINSIZE	MINSIZE for short form
cutEnd	how many nucleotides should be removed from the end before search, 0.1 means 10 percent.
search_point_START	start point for searching
search_point_END	end point for searching
two_way	Search the proximal site from both direction or not.

Value

a list

Author(s)

Jianhong Ou

See Also

proximalAdj, polishCPs, proximalAdjByPWM, proximalAdjByCleanUpdTSeq, PAscore,PAscore2

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