generate_self_merged_peaks: Merge a set of peaks

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Merge a set of peaks

Description

Given a self-similarity table of peaks, identify peaks that should be merged. Merged peaks are taken as the union of the two peaks. For two given peaks, A and B, they will be merged if at least one has some x% (75% by default) or more overlap with the other, and the other has at least x-(y*x)% overlap where y is a percentage of allowed variance (25% by default)

Usage

generate_self_merged_peaks(
  apa.similarity.table,
  sim.thresh = 0.75,
  allow.match.var = 0.25,
  return.type = "peak_list"
)

Arguments

apa.similarity.table	the set of peaks to merge
sim.thresh	The required similarity threshold for merging (default: 0.75)
allow.match.var	The allowance for deviation from the sim.thresh for comparison peaks (default: 0.25)
return.type	Whether to return a full table of results or simply a vector of merged peaks

Value

a table of merged peaks with original merged peaks or a vector of merged peaks

Examples

## Not run: 
generate_self_merged_peaks(apa.similarity.table)

## End(Not run)

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.