combine_derep: Combine DADA2 'derep' objects into master map

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

Description

Combine DADA2 derep objects into master map

Usage

combine_derep(dereps, .data = NULL, ...)

Arguments

dereps	a (possibly named) list of (derep objects), or a tibble with a column "derep" containing such a list.
.data	a tibble with the same number of rows as the length of dereps.
...	additional columns to add to the output.

Details

To be useful for further analysis, each sequence should be uniquely identified. This can be done in several ways:

• dereps is a named list with unique names;

• dereps is a tibble with columns (other than "derep") which uniquely identify the rows;

• .data is provided and its rows are unique; or

• ... is provided and its combinations are unique.

Value

list with two members:

$map (tibble)

with columns: "file" (character), "idx" (integer), and "map" (integer), giving the mapping from the "idx"th sequence in "file" to a sequence in "fasta"

$fasta ( DNAStringSet-class)

all unique sequences; the name of each sequence is an integer which matches a value in map$newmap

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