Add sequence data to a strollur object

Usage

xdev_add_sequences(
  data,
  table,
  reference = NULL,
  sequence_name = "sequence_name",
  sequence = "sequence",
  comment = "comment",
  verbose = TRUE
)

Arguments

data: a strollur object
table: a data.frame containing names, sequences(optional) and comments(optional).
reference: a list created by the function new_reference. Optional.
sequence_name: a string containing the name of the column in 'table' that contains the sequence names. Default column name is 'sequence_name'.
sequence: a string containing the name of the column in 'table' that contains the sequence nucleotide strings. Default column name is 'sequence'.
comment: a string containing the name of the column in 'table' that contains the sequence comments. Default column name is 'comment'.
verbose: a boolean whether or not you want progress messages. Default = TRUE.

Value

an updated strollur object

Examples


 data <- strollur::new_dataset("miseq_sop")
 fasta_data <- strollur::read_fasta(strollur_example("final.fasta.gz"))
 strollur::xdev_add_sequences(data, fasta_data)
#> Added 2425 sequences.
#> miseq_sop:
#> 
#>             starts ends nbases ambigs polymers numns numseqs
#> Minimum:         1  375    249      0        3     0    1.00
#> 2.5%-tile:       1  375    252      0        4     0   61.60
#> 25%-tile:        1  375    252      0        4     0  607.00
#> Median:          1  375    253      0        4     0 1213.00
#> 75%-tile:        1  375    253      0        5     0 1819.00
#> 97.5%-tile:      1  375    254      0        6     0 2364.40
#> Maximum:         1  375    256      0        6     0 2425.00
#> Mean:            1  375    252      0        4     0 1213.00
#> 
#> Number of unique seqs: 2425 
#> Total number of seqs: 2425 
#> 
#> 

# With the additional parameters to add information about the reference

 data <- strollur::new_dataset("miseq_sop")
 fasta_data <- strollur::read_fasta(strollur_example("final.fasta.gz"))

 strollur::xdev_add_sequences(data, fasta_data,
               new_reference("silva.bacteria.fasta",
               "1.38.1",
               "alignment by mothur2 v1.0 using default options",
               "https://mothur.org/wiki/silva_reference_files/"))
#> Added 2425 sequences.
#> Added 1 resource references.
#> miseq_sop:
#> 
#>             starts ends nbases ambigs polymers numns numseqs
#> Minimum:         1  375    249      0        3     0    1.00
#> 2.5%-tile:       1  375    252      0        4     0   61.60
#> 25%-tile:        1  375    252      0        4     0  607.00
#> Median:          1  375    253      0        4     0 1213.00
#> 75%-tile:        1  375    253      0        5     0 1819.00
#> 97.5%-tile:      1  375    254      0        6     0 2364.40
#> Maximum:         1  375    256      0        6     0 2425.00
#> Mean:            1  375    252      0        4     0 1213.00
#> 
#> Number of unique seqs: 2425 
#> Total number of seqs: 2425 
#> 
#> Total number of resource references: 1 
#> 

# You can also add references using the `strollur::xdev_add_references`
# function.