search_distalCPs: search distal CP sites

View source: R/13.search_distalCPs.R

search_distalCPsR Documentation

search distal CP sites

Description

search distal CP sites

Usage

search_distalCPs(
  chr.cov.merge,
  conn_next_utr3,
  curr_UTR,
  window_size,
  depth.weight,
  long_coverage_threshold,
  background,
  z2s
)

Arguments

chr.cov.merge

merged coverage data for a given chromosome

conn_next_utr3

A logical(1) vector, indicating whether joint to next 3UTR or not (used by remove_convergentUTR3s())

curr_UTR

GRanges of 3' UTR for a given chromosome

window_size

An integer(1) vector, the window size for novel distal or proximal CP site searching. default: 100.

depth.weight

A named vector. One element of an output of setup_CPsSearch() for coverage depth weight, which is the output of get_depthWeight()

long_coverage_threshold

An integer(1) vector, specifying the cutoff threshold of coverage for the terminal of long form 3' UTRs. If the coverage of first 100 nucleotides is lower than coverage_threshold, that transcript will be not considered for further analysis. Default, 2.

background

A character(1) vector, the range for calculating cutoff threshold of local background. It can be "same_as_long_coverage_threshold", "1K", "5K","10K", or "50K".

z2s

one element of an output of setup_CPsSearch() for Z-score cutoff values, which is the output of get_zScoreCutoff()

Value

a list #'

  • dCPs, a data frame converted from GRanges

  • chr.cov.merge, depth-normalized sample/condition specific coverage

  • next.exon.gap, all-in-one collapsed, refined next.exon.gap coverage

  • annotated.utr3,all-in-one collapsed coverage for annotated proximal UTRs

Author(s)

Jianhong Ou

See Also

get_PAscore2()


jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.