search_proximalCPs {InPAS} | R Documentation |
search proximal CPsites
search_proximalCPs( CPs, curr_UTR, window_size, MINSIZE, cutEnd, search_point_START, search_point_END, two_way = FALSE )
CPs |
output from |
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. |
a list
Jianhong Ou
adjust_proximalCPs()
, polish_CPs()
,adjust_proximalCPsByPWM()
,
adjust_proximalCPsByNBC()
, get_PAscore()
, get_PAscore2()