The object class returned by dada

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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.

  • $call: The function call used for this invocation of dada.

See Also

dada

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