Description Usage Arguments Details Value
This function is intended to be run on reads from a single sub-region/domain, which have been clustered using a linked sub-region/domain; for instance, ITS1 reads clustered based on identity/similarity of the linked ITS2 reads.
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asvs |
( |
raw |
( |
maxdist |
( |
allow_map |
( |
allow_consensus |
( |
allow_raw |
( |
... |
passed to |
If some of the target reads have been mapped to ASVs, then
map_or_consensus
attempts to map additional raw reads to the same
ASVs using a (potentially) more relaxed criteria than
dada
. This is implemented in
map_to_best_asv
.
If, on the other hand, none of the input sequences have been assigned to an
ASV, then the entire group is taken to represent one cluster, and a consensus
sequence for the cluster is determined using cluster_consensus
.
This process will remove outliers (generally chimeric in origin) and assign
NA_character_
to the associated reads, as well as any reads which are
already NA
due to quality filtering, failed region extraction, etc.
a character
vector the same length as asvs
, which has
the closest ASV for each read if any ASVs are non-missing, or the cluster
consensus values for raw reads which were non-missing and not outliers.
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