generate_merged_peak_table: Merge peaks across data-sets based on a reference

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

Merge peaks across data-sets based on a reference

Description

Given a reference data-set, a list of data-sets for merging and set of merged peaks from the referece, identify peaks that should be merged. Merged peaks are taken as the union of the peaks to be merged. 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_merged_peak_table(
  dataset.1,
  peak.dataset.list,
  self.merged.peaks.list,
  sim.thresh = 0.75,
  allow.match.var = 0.25,
  ncores = 1
)

Arguments

dataset.1	the reference peak data-set
peak.dataset.list	a list of peak data-sets
self.merged.peaks.list	the set of self-merged peaks from the reference data-set
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)
ncores	Number of cores for multithreading

Value

a data-frame containing peaks, their class (merged or unique) and the original peak from the reference

Examples

## Not run: 
     generate_merged_peak_table(dataset.1, peak.dataset.table, self.merged.peaks.list)
     
     
     
     
     
 
## End(Not run)

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