A basic Illumina sequencer class

This class implements a basic model for Illumina sequencers.

This method builds a basic Illumina sequencer model.

Arguments

error_rate

The error rate of the sequencer model.

random_quality_scores

A Boolean flag to enable a basic non-constant quality score model. When it is set to FALSE, all the bases with no sequencing errors have the same quality score. The random quality score model increases the computation time of about 70%. (default: TRUE)

Value

A basic Illumina sequencer model.

Details

It specifies a simulated sequencing error rate and the simulated sequencing errors will occurs according to that rate.

See also

simulate_seq(), simulate_normal_seq(), and vignette("sequencing") for usage examples

Examples

# build a sequencer model having error rate 4e-3
sequencer <- BasicIlluminaSequencer(error_rate=4e-3)
sequencer
#> Basic Illumina Sequencer (platform: "ILLUMINA" error rate: 0.004000 random quality scores)

# build a sequencer model having error rate 4e-3 and set the seed to 5
sequencer <- BasicIlluminaSequencer(error_rate=4e-3, seed=5)
#> Error in BasicIlluminaSequencer(error_rate = 0.004, seed = 5): unused argument (seed = 5)
sequencer
#> Basic Illumina Sequencer (platform: "ILLUMINA" error rate: 0.004000 random quality scores)