summarize_sread: Summarize one or more reads as a 'tibble'.

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

Description

Summarize one or more reads as a tibble.

Usage

summarize_sread(sread, ..., max_ee)

Arguments

sread	(ShortReadQ object or list of such objects) as produced by readFastq.
...	(any vector) additional columns to add to the output tibble. These should have length 1 or, if sread is a named list of ShortReadQ, the length of sread. Recycling behavior is as in tibble. Avoid the name "name" if sread is a named list
max_ee	(numeric) filter out reads with expected error greater than max_ee. Default: Inf (no filtering)

Value

a tibble with columns:

$seq_id (character)

sequence IDs, typically from the input fastq

$seq (character)

the actual sequence reads

$name (character)

the name of the source ShortReadQ, if sread was a list. Otherwise absent.

...

any other arguments passed to summarize_sread.

If the input was empty, not a valid ShortReadQ, or no sequences passed filtering, a tibble with zero rows is returned.

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