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

Source: R/dada_phyloseq.R
physeq_or_string_to_dna.Rd

lifecycle-stable

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)

See also

Biostrings::DNAStringSet()

Author

Adrien Taudière

Examples


dna <- physeq_or_string_to_dna(data_fungi)
dna
#> DNAStringSet object of length 1420:
#>        width seq                                            names               
#>    [1]   312 AAATGCGATAAGTAATGTGAAT...TAGGAATACCCGCTGAACTTA ASV2
#>    [2]   301 AAATGCGATAAGTAATGTGAAT...TAGGAATACCCGCTGAACTTA ASV6
#>    [3]   349 AAATGCGATAAGTAATGTGAAT...TGGGACTACCCGCTGAACTTA ASV7
#>    [4]   357 AAATGCGATAAGTAATGTGAAT...TGGGACTACCCGCTGAACTTA ASV8
#>    [5]   300 AAATGCGATAAGTAATGTGAAT...TAGGAATACCCGCTGAACTTA ASV10
#>    ...   ... ...
#> [1416]   339 AATCGCGATATGTAGTGTGATC...GGGATTACCCGCTGAACTTAA ASV1712
#> [1417]   356 GAAACGCGATATGTAATCGTGC...TAGGACTACCCGCTGAACTTA ASV1714
#> [1418]   420 AACTGCGAAACGTCATGTGACC...TAAGGATACCCGCTGAACTTA ASV1716
#> [1419]   337 GAAGTGCGATAAGCAATGCGAA...CAGGATCACCCGCTGAACTTA ASV1719
#> [1420]   260 AAACGCGAAAAGTGTTATGATG...AAGATCACCCGCTGAACTTAA ASV1726

sequences_ex <- c(
  "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTAATAACGAATTCATTGAATCA",
  "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTT",
  "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAGAGGTG",
  "TACCTATGTTGCCTTGGCGGCTAAACCTACC",
  "CGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCATGAGGTG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
  "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG"
)
dna2 <- physeq_or_string_to_dna(dna_seq = sequences_ex)
dna2
#> DNAStringSet object of length 9:
#>     width seq
#> [1]    73 TACCTATGTTGCCTTGGCGGCTAAACCTACCCGG...ATGGGGCGAATTAATAACGAATTCATTGAATCA
#> [2]    70 TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTT
#> [3]    66 TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAGAGGTG
#> [4]    31 TACCTATGTTGCCTTGGCGGCTAAACCTACC
#> [5]    58 CGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCATGAGGTG
#> [6]    40 GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG
#> [7]    40 GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG
#> [8]    40 GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG
#> [9]    40 GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG