find_all_region_chimeras: Find chimeras in adjacent variable-conserved-variable domain...

In brendanf/tzara: Cluster long amplicons using dada2 denoising on variable regions

Description

Find chimeras in adjacent variable-conserved-variable domain triplets

Usage

find_all_region_chimeras(
  region_table,
  order,
  sample_column = NULL,
  read_column = "read_id",
  chimera_offset = 0,
  ...
)

Arguments

region_table	(data.frame containing all the regions in order)
order	(character with the regions to check)
sample_column	(character scalar) extra column in region_table which identifies different samples; if present, use isBimeraDenovoTable instead of isBimeraDenovo.
read_column	(character scalar) column in region_table which identifies different reads.
chimera_offset	(integer scalar) use 1 if the first region is conserved.
...	passed to find_region_chimeras.

Value

a tibble with columns:

chimset

(list of character) the set of regions (usually 3) which were checked in each row.

chims

list of character) the sequence IDs of the reads which were identified as chimeric for each set of regions

brendanf/tzara documentation built on March 11, 2021, 5:40 a.m.