Description Usage Arguments Details Value
The sequences from each denoised sub-region/domain are concatenated to create
a denoised sequence
for the long region. Additionally, de-novo bimera detection is performed
using isBimeraDenovo
or
isBimeraDenovoTable
on
sets of three consecutive sub-regions/domains; in the intended application,
these sets will be variable–conserved–variable.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | reconstruct(
seqtabs,
regions = names(seqtabs),
regions_regex = NULL,
regions_replace = NULL,
output = "concat",
use_output = c("first", "second", "no"),
order = regions,
read_column = "seq_id",
asv_column = "dada_seq",
rawtabs = seqtabs,
raw_column = NULL,
raw_regions = names(rawtabs),
sample_column = NULL,
sample_regex = NULL,
sample_replace = NULL,
chimera_offset = 0,
allow_map = TRUE,
allow_consensus = TRUE,
allow_raw = FALSE,
...
)
|
seqtabs |
( |
regions |
( |
regions_regex |
( |
regions_replace |
( |
output |
( |
use_output |
(one of |
order |
( |
read_column |
( |
asv_column |
( |
rawtabs |
( |
raw_column |
( |
raw_regions |
( |
sample_column |
( |
sample_regex |
( |
sample_replace |
( |
chimera_offset |
( |
allow_map |
( |
allow_consensus |
( |
allow_raw |
( |
... |
additional arguments passed to |
When not all sub-regions/domains for a given read have been successfully
denoised with DADA, then the missing regions are constructed using
cluster_consensus
.
a tibble
with column "seq_id
" and
sample_column
(if given), as well as one column for each value
of regions
and output
, representing the
sub-regions/domains and the concatenated full region.
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