Add FASTQ data to a
strollur object.
Scores are stored as vector
Usage
xdev_add_sequence_fastq_scores(
data,
table,
reference = NULL,
sequence_name = "sequence_name",
sequence = "sequence",
quality_score = "quality_score",
verbose = TRUE
)Arguments
- data
- table
a data.frame containing FASTQ 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'.
- sequence
a string containing the name of the column in 'table' that contains the sequence nucleotide strings. Default column name is 'sequence'. (Optional)
- quality_score
a string containing the name of the column in 'table' that contains the quality scores stored as vector
. Default column name is 'quality_score'. - verbose
a logical whether or not you want progress messages. Default = TRUE.
Value
an updated strollur object
Examples
table <- strollur::read_fastq(strollur_example("tiny.fastq.gz"))
data <- strollur::new_dataset("example")
strollur::xdev_add_sequence_fastq_scores(data, table)
#> Added 3 sequences.
#> 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
#>
#>