xdev_add_sequences

Add sequence data to a strollur object

Usage

xdev_add_sequences(
  data,
  table,
  reference = NULL,
  sequence_name = "sequence_names",
  sequence = "sequences",
  comment = "comments",
  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_names'.

sequence,

a string containing the name of the column in 'table' that contains the sequence nucleotide strings. Default column name is 'sequences'.

comment,

a string containing the name of the column in 'table' that contains the sequence comments. Default column name is 'comments'.

verbose,

a boolean whether or not you want progress messages. Default = TRUE.

Value

double containing the number of sequences added

Examples

 data <- new_dataset("miseq_sop")
 fasta_data <- read_fasta(strollur_example("final.fasta.gz"))
 xdev_add_sequences(data, fasta_data)
#> Added 2425 sequences.
#> [1] 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.
#> [1] 2425

# You can also add references using the 'add_references' function.