Description Usage Arguments Slots

This class is deprecated and will be defunct in a future release.

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## S4 method for signature 'TrioSet'
pedigree(object)
## S4 method for signature 'TrioSet'
show(object)
## S4 method for signature 'TrioSet'
mindist(object)
## S4 replacement method for signature 'TrioSet,matrix'
mindist(object) <- value
## S4 method for signature 'TrioSet'
dim(x)
## S4 method for signature 'TrioSet'
trios(object)
## S4 method for signature 'TrioSet,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]
## S4 method for signature 'TrioSet,GRanges'
MAP(
object,
ranges,
transition_param = TransitionParam(),
emission_param = EmissionParam(),
mdThr = 0.9,
...
)
## S4 method for signature 'ff_array,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]
``` |

`object` |
a |

`value` |
a |

`x` |
a |

`i` |
a numeric vector for subsetting rows (optional) |

`j` |
a numeric vector for subsetting trios (optional) |

`...` |
additional arguments passed to subsetting methods for matrices and data frames |

`drop` |
logical. Whether to simplify matrices to numeric vectors. This should be left as FALSE. |

`ranges` |
a |

`transition_param` |
an object of class |

`emission_param` |
an object of class |

`mdThr` |
the minimum absolute value of the minimum distance
segment mean. Segments with means below |

`fatherPhenoData`

`AnnotatedDataFrame`

containing covariates for the father`motherPhenoData`

`AnnotatedDataFrame`

containing covariates for the mother`pedigree`

an object of class

`Pedigree`

`mindist`

a numeric matrix of the minimum distance for each trio, or NULL

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