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 <- new_dataset("miseq_sop")
fasta_data <- read_fasta(strollur_example("final.fasta.gz"))
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 61.62
#> 25%-tile: 1 375 252 0 4 0 607.25
#> Median: 1 375 253 0 4 0 1213.50
#> 75%-tile: 1 375 253 0 5 0 1819.75
#> 97.5%-tile: 1 375 254 0 6 0 2365.38
#> Maximum: 1 375 256 0 6 0 2425.00
#> Mean: 1 375 252 0 4 0 0.00
#>
#> Number of unique seqs: 2425
#> Total number of seqs: 2425
#>
#>
# With the additional parameters to add information about the reference
data <- new_dataset("miseq_sop")
fasta_data <- read_fasta(strollur_example("final.fasta.gz"))
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 61.62
#> 25%-tile: 1 375 252 0 4 0 607.25
#> Median: 1 375 253 0 4 0 1213.50
#> 75%-tile: 1 375 253 0 5 0 1819.75
#> 97.5%-tile: 1 375 254 0 6 0 2365.38
#> Maximum: 1 375 256 0 6 0 2425.00
#> Mean: 1 375 252 0 4 0 0.00
#>
#> Number of unique seqs: 2425
#> Total number of seqs: 2425
#>
#> Total number of resource references: 1
#>
# You can also add references using the 'add_references' function.