filterCombs: `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]))