search_proximalCPs: search proximal CPsites

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

search proximal CPsites

Description

search proximal CPsites

Usage

search_proximalCPs(
  CPs,
  curr_UTR,
  window_size,
  MINSIZE,
  cutEnd = NA,
  search_point_START,
  search_point_END = NA,
  filter.last = TRUE,
  DIST2END = 1000
)

Arguments

CPs	output from search_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 or an integer(1) greater than 1, specifying the percentage of or the number of nucleotides should be removed from the end before search for proximal CP sites, 0.1 means 10 percent. It is recommended to use an integer great than 1, such as 200, 400 or 600, because read coverage at 3' extremities is determined by fragment size due to RNA fragmentation and size selection during library construction.
search_point_START	An integer, specifying the start position to calculate MSE
search_point_END	A numeric(1) between 0 and 1 or an integer(1) greater than 1, specifying the percentage of or the number of nucleotides should not be excluded from the end to calculate MSE.
filter.last	A logical(1), whether to filter out the last valley, which is likely the 3' end of the longer 3' UTR if no novel distal CP site is detected and the 3' end excluded by setting cutEnd/search_point_END is small.
DIST2END	An integer, specifying a cutoff of the distance between last valley and the end of the 3' UTR (where MSE of the last base is calculated). If the last valley is closer to the end than the specified distance, it will be not be considered because it is very likely due to RNA coverage decay at the end of mRNA. Default is 1200. User can consider a value between 1000 and 1500, depending on the library preparation procedures: RNA fragmentation and size selection.

Value

a list

Author(s)

Jianhong Ou

See Also

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

jianhong/InPAS documentation built on Oct. 27, 2023, 2:13 p.m.