searchProximalCPs {InPAS}R Documentation

search proximal CPsites

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


[Package InPAS version 1.22.0 Index]