search_proximalCPs {InPAS}R Documentation

search proximal CPsites

Description

search proximal CPsites

Usage

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

Arguments

CPs

output from search_distalCPs() or adjust_distalCPs()

curr_UTR

GRanges for current 3' UTR

window_size

window size

MINSIZE

MINSIZE for short form

cutEnd

a numeric(1) between 0 and 1. The percentage of 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

adjust_proximalCPs(), polish_CPs(),adjust_proximalCPsByPWM(), adjust_proximalCPsByNBC(), get_PAscore(), get_PAscore2()


[Package InPAS version 2.0.0 Index]