dada-class {dada2} | R Documentation

## The object class returned by `dada`

### Description

A multi-item List with the following named values...

- $denoised: Integer vector, named by sequence valued by abundance, of the denoised sequences.

- $clustering: An informative data.frame containing information on each cluster.

- $sequence: A character vector of each denoised sequence. Identical to names($denoised).

- $quality: The average quality scores for each cluster (row) by position (col).

- $map: Integer vector that maps the unique (index of derep$unique) to the denoised sequence (index of dada$denoised).

- $birth_subs: A data.frame containing the substitutions at the birth of each new cluster.

- $trans: The matrix of transitions by type (row), eg. A2A, A2C..., and quality score (col) observed in the final output of the dada algorithm.

- $err_in: The err matrix used for this invocation of dada.

- $err_out: The err matrix estimated from the output of dada. NULL if err_function not provided.

- $opts: A list of the dada_opts used for this invocation of dada.

### See Also

`dada`

[Package dada2 version 1.20.0 Index]