assignSpecies_mod: Return long-form species assignments with DADA2's...
In ammararuby/MButils: Utility functions for DNA metabarcoding
View source: R/assignSpecies_mod.R
assignSpecies_mod R Documentation
Return long-form species assignments with DADA2's assignSpecies
Description
This function is a modification of DADA2's assignSpecies,
which uses exact matching against a reference fasta to identify the
genus-species binomial classification of the input sequences. Where the
original function run with allowMultiple = TRUE returns a
concatenated string of all exactly matched species, results are returned
here as distinct rows, one per match.
Usage
assignSpecies_mod(seqs, refFasta, tryRC = FALSE, n = 2000)
Arguments
seqs
A character vector of the sequences to be assigned
refFasta
The path to the reference fasta file, or an R connection. Can
be compressed. This reference fasta file should be formatted so that the ID
lines correspond to the genus-species of the associated sequence:
>SeqID genus species ACGAATGTGAAGTAA......
tryRC
(Optional). Default FALSE. If TRUE, the reverse-complement of
each sequences will also be tested for exact matching to the reference
sequences.
n
(Optional). Default 2000. The number of sequences to perform
assignment on at one time. This controls the peak memory requirement so
that large numbers of sequences are supported.
Value
A two-column data frame matching ASVs to their exact match in the
reference, with multiple matches indicated by the presence of more than one
row per ASV.
ammararuby/MButils documentation built on Jan. 29, 2023, 11:13 a.m.
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View source: R/assignSpecies_mod.R
| assignSpecies_mod | R Documentation |
Return long-form species assignments with DADA2's assignSpecies
Description
This function is a modification of DADA2's assignSpecies,
which uses exact matching against a reference fasta to identify the
genus-species binomial classification of the input sequences. Where the
original function run with allowMultiple = TRUE returns a
concatenated string of all exactly matched species, results are returned
here as distinct rows, one per match.
Usage
assignSpecies_mod(seqs, refFasta, tryRC = FALSE, n = 2000)
Arguments
seqs |
A character vector of the sequences to be assigned |
refFasta |
The path to the reference fasta file, or an R connection. Can be compressed. This reference fasta file should be formatted so that the ID lines correspond to the genus-species of the associated sequence: >SeqID genus species ACGAATGTGAAGTAA...... |
tryRC |
(Optional). Default FALSE. If TRUE, the reverse-complement of each sequences will also be tested for exact matching to the reference sequences. |
n |
(Optional). Default 2000. The number of sequences to perform assignment on at one time. This controls the peak memory requirement so that large numbers of sequences are supported. |
Value
A two-column data frame matching ASVs to their exact match in the reference, with multiple matches indicated by the presence of more than one row per ASV.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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