TrioSet-class {MinimumDistance} | R Documentation

## Deprecated class for storing low-level genomic data for trios

### Description

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

### Usage

    ## 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]

### Arguments

`object` | a `TrioSet` object
`value` | a `matrix`
`x` | a `TrioSet` object
`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 `GRanges` object
`transition_param` | an object of class `TransitionParam`
`emission_param` | an object of class `EmissionParam`
`mdThr` | the minimum absolute value of the minimum distance segment mean. Segments with means below `mdThr` in absolute value will not be called as they are unlikely to be de novo.

### Slots

`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

[Package MinimumDistance version 1.36.0 Index]