physeq_or_string_to_dna: Return a DNAStringSet object from either a character vector...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Return a DNAStringSet object from either a character vector of DNA sequences or the refseq slot of a phyloseq-class object

Description

Internally used in vsearch_clustering(), swarm_clustering() and postcluster_pq().

Usage

physeq_or_string_to_dna(physeq = NULL, dna_seq = NULL)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
dna_seq	You may directly use a character vector of DNA sequences in place of physeq args. When physeq is set, dna sequences take the value of physeq@refseq

Value

An object of class DNAStringSet (see the Biostrings::DNAStringSet() function)

Author(s)

Adrien Taudière

See Also

Biostrings::DNAStringSet()

Examples

dna <- physeq_or_string_to_dna(data_fungi)
dna

sequences_ex <- c(
  "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTAATAACGAATTCATTGAATCA",
  "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTT",
  "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAGAGGTG",
  "TACCTATGTTGCCTTGGCGGCTAAACCTACC",
  "CGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCATGAGGTG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG"
)
dna2 <- physeq_or_string_to_dna(dna_seq = sequences_ex)
dna2

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.