Add quality data to a strollur object

Add quality data to a strollur object.

Usage

xdev_assign_sequence_quality_scores(
  data,
  table,
  reference = NULL,
  sequence_name = "sequence_name",
  quality_score = "quality_score",
  verbose = TRUE
)

Arguments

data

a strollur object

table

a data.frame containing quality data you are trying to add

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'.

quality_score

a string containing the name of the column in 'table' that contains the quality scores. Default column name is 'quality_score'.

verbose

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

Value

an updated strollur object

Examples

qual_table <- strollur::read_quality(strollur_example("tiny.qual"))
fasta_table <- strollur::read_fasta(strollur_example("tiny.fasta"))

data <- strollur::new_dataset("example")
strollur::xdev_add_sequences(data, fasta_table)
#> Added 3 sequences.
#> example:
#> 
#>             starts ends nbases ambigs polymers numns numseqs
#> Minimum:         1  251    251      0        4     0    1.00
#> 2.5%-tile:       1  251    251      0        4     0    1.05
#> 25%-tile:        1  251    251      0        4     0    1.50
#> Median:          1  251    251      0        4     0    2.00
#> 75%-tile:        1  251    251      0        4     0    2.50
#> 97.5%-tile:      1  251    251      0        4     0    2.95
#> Maximum:         1  251    251      1        4     1    3.00
#> Mean:            1  251    251      0        4     0    2.00
#> 
#> Number of unique seqs: 3 
#> Total number of seqs: 3 
#> 
#> 
strollur::xdev_assign_sequence_quality_scores(data, qual_table)
#> Assigned 3 quality scores.
#> example:
#> 
#>             starts ends nbases ambigs polymers numns numseqs
#> Minimum:         1  251    251      0        4     0    1.00
#> 2.5%-tile:       1  251    251      0        4     0    1.05
#> 25%-tile:        1  251    251      0        4     0    1.50
#> Median:          1  251    251      0        4     0    2.00
#> 75%-tile:        1  251    251      0        4     0    2.50
#> 97.5%-tile:      1  251    251      0        4     0    2.95
#> Maximum:         1  251    251      1        4     1    3.00
#> Mean:            1  251    251      0        4     0    2.00
#> 
#> Number of unique seqs: 3 
#> Total number of seqs: 3 
#> 
#> 

data
#> example:
#> 
#>             starts ends nbases ambigs polymers numns numseqs
#> Minimum:         1  251    251      0        4     0    1.00
#> 2.5%-tile:       1  251    251      0        4     0    1.05
#> 25%-tile:        1  251    251      0        4     0    1.50
#> Median:          1  251    251      0        4     0    2.00
#> 75%-tile:        1  251    251      0        4     0    2.50
#> 97.5%-tile:      1  251    251      0        4     0    2.95
#> Maximum:         1  251    251      1        4     1    3.00
#> Mean:            1  251    251      0        4     0    2.00
#> 
#> Number of unique seqs: 3 
#> Total number of seqs: 3 
#> 
#>