filterCombs: 'filterCombs' Remove sequences likely resulting from...

In dowser: B Cell Receptor Phylogenetics Toolkit

filterCombs Remove sequences likely resulting from oversequencing and PCR error This removes "comb" structures in trees which are flat polytomies with low duplicate counts radiating out from a single node with a much higher duplicate count. Adapted from https://bitbucket.org/kleinstein/projects/src/master/Hoehn2022/isotype_analysis/treesAndSwitches_dowser.R

Description

filterCombs Remove sequences likely resulting from oversequencing and PCR error This removes "comb" structures in trees which are flat polytomies with low duplicate counts radiating out from a single node with a much higher duplicate count. Adapted from https://bitbucket.org/kleinstein/projects/src/master/Hoehn2022/isotype_analysis/treesAndSwitches_dowser.R

Usage

filterCombs(
  data,
  dup_count_thresh = 100,
  exponent = 1,
  id = "sequence_id",
  seq = "sequence_alignment",
  clone = "clone_id",
  duplicate = "duplicate_count",
  gap = 0
)

Arguments

data	data.frame containing the AIRR or Change-O data for a clone. See Details for the list of required columns and their default values.
dup_count_thresh	Minimum duplicate count to be considered a 'comb'
exponent	determines whether a child sequence is to be cut. Based on duplicate_count ratio of child node to parent exponent=1 -> cutting 1/100 (child/parent) at 1 Hamming dist, 1/1000 at 2 dist, while exponent=2 -> cutting 1/1000 (child/parent) at distance 1.
id	name of the column containing sequence identifiers.
seq	name of the column containing observed DNA sequences. All sequences in this column must be multiple aligned.
clone	name of the column containing the identifier for clones.
duplicate	name of the column containing the number of duplicates for this sequence.
gap	gap penalty for Hamming distance. gap=0 means gaps ignored.

Details

Formula for cutting a child sequence is: child[[duplicate]]/parent[[duplicate]] < 10^(-(exponent + Hamming distance[child, parent]))

dowser documentation built on Aug. 20, 2026, 5:06 p.m.