search_distalCPs: search distal CP sites

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

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 Oct. 27, 2023, 2:13 p.m.