rna_majiq.ExperimentThresholds

class rna_majiq.ExperimentThresholds

Thresholds on intron/junction coverage for inclusion in splicegraph

__init__(self: rna_majiq.internals.ExperimentThresholds, minreads: int = 3, mindenovo: int = 5, minpos: int = 2, max_pctbins: float = 0.6000000238418579, junction_acceptance_probability: float = 0.5, intron_acceptance_probability: float = 0.949999988079071) → None

Thresholds on intron/junction coverage for inclusion in SpliceGraph

Methods

__init__(self[, minreads, mindenovo, ...])	Thresholds on intron/junction coverage for inclusion in SpliceGraph
intron_thresholds_generator(self, total_bins)	Create IntronThresholdsGenerator for intron thresholds by length

Attributes

intron_acceptance_probability	Intron thresholds pass per-position readrate with probability
junction_acceptance_probability	Set intron thresholds to match junction readrate with probability
max_pctbins	Maximum percentage of bins to require coverage in for intron to pass
mindenovo	Minimum number of reads for a denovo junction to pass
minpos	Minimum number of nonzero positions for a junction to pass
minreads	Minimum number of reads for an annotated junction to pass