Description Usage Arguments Value Examples

User Constructor for class. Call limits are set as default to pass.

1 2 3 4 5 6 7 | ```
VCFQAParam(homref.limits = c(-Inf, Inf), het.limits = c(-Inf, Inf),
homvar.limits = c(-Inf, Inf), percenthets.limits = c(-Inf, Inf),
titv.noncoding.limits = c(-Inf, Inf), titv.coding.limits = c(-Inf, Inf),
readdepth.target = -1, readdepth.limits = c(-Inf, Inf),
readdepth.percent.limits = 0, gq.limit = 0, masked.limits = c(-Inf,
Inf), non.masked.limits = c(-Inf, Inf), het.gap.limits = rep(Inf, 24),
count.limits = c(-Inf, Inf), gq.filter = 0, dp.filter = -1)
``` |

`homref.limits` |
lower limit, upper limit, number of homozygous reference |

`het.limits` |
lower limit, upper limit, number of heterozygous calls |

`homvar.limits` |
lower limit, upper limit, number of homozygous alternative |

`percenthets.limits` |
lower limit, upper limit, Number of Heterozgyous / (Total Number of Counts) or percent het |

`titv.noncoding.limits` |
lower limit, upper limit, Transition transversion ratio in noncoding regions |

`titv.coding.limits` |
lower limit, upper limit, Transition transversion ratio in coding regions |

`readdepth.target` |
The sequencing depth target (eg 30x) |

`readdepth.limits` |
lower limit, upper limit, Mean read depth |

`readdepth.percent.limits` |
lower limit, upper limit, Percent read depth in target (50 percent to 200 percent of target read depth) |

`gq.limit` |
lower limit, Mean genotype quality (does not make sense to have an upper limit) |

`masked.limits` |
lower limit, upper limit, (Number of heterozygous in self chained regions)/(Total number of heterozygotes) |

`non.masked.limits` |
lower limit, upper limit, (Number of heterozygous in non-self chained regions)/(Total number of heterozygotes) |

`het.gap.limits` |
lower limit, upper limit, Largest gap within chromosome between two heterozygous calls |

`count.limits` |
lower limit, upper limit, total number of counts |

`gq.filter` |
filter for the VCF file on genotype quality (eg only GQ > 90) |

`dp.filter` |
filter for the VCF file on read depth (eg only DP > 0) |

Object of class VCFQAParam

1 | ```
vcfparams <- VCFQAParam(count.limits=c(3014580000, Inf), readdepth.target = 30)
``` |

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