Set neucleotide sequence string in a strollur object

Designed with package integration in mind, the set sequences function allows you to change the nucleotide strings of sequences in a strollur object. For example, set_sequences may be used after alignment to overwrite the unaligned sequences with aligned sequences.

Usage

xdev_set_sequences(
  data,
  sequence_names,
  sequences,
  comments = as.character(c())
)

Arguments

data

a strollur object

sequence_names

a vector of strings containing sequence names

sequences

a vector of strings containing sequence nucleotide strings

comments

a vector of strings containing sequence comments. (Optional)

Value

an updated strollur object

Examples

data <- strollur::new_dataset(dataset_name = "my_dataset")

strollur::xdev_add_sequences(data,
              table = data.frame(sequence_name = c("seq1", "seq2",
                                                  "seq3", "seq4")))
#> Added 4 sequences.
#> my_dataset:
#> 
#> 
#> Number of unique seqs: 4 
#> Total number of seqs: 4 
#> 
#> 

strollur::xdev_set_sequences(data,
                   sequence_names = c("seq1", "seq2","seq3", "seq4"),
                   sequences = c("ATTGC", "ACTGC", "AGTGC", "TTTGC"))
#> my_dataset:
#> 
#>             starts ends nbases ambigs polymers numns numseqs
#> Minimum:         1    5      5      0        1     0    1.00
#> 2.5%-tile:       1    5      5      0        1     0    1.07
#> 25%-tile:        1    5      5      0        1     0    1.75
#> Median:          1    5      5      0        1     0    2.50
#> 75%-tile:        1    5      5      0        2     0    3.25
#> 97.5%-tile:      1    5      5      0        2     0    3.92
#> Maximum:         1    5      5      0        3     0    4.00
#> Mean:            1    5      5      0        1     0    2.50
#> 
#> Number of unique seqs: 4 
#> Total number of seqs: 4 
#> 
#>