TrioSetList-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 'TrioSetList,RangedSummarizedExperiment'
    coerce(from, to)

    ## S4 method for signature 'TrioSetList'
    pedigree(object)

    ## S4 method for signature 'TrioSetList'
    trios(object)

    ## S4 method for signature 'TrioSetList'
    offspringNames(object)

    ## S4 method for signature 'TrioSetList,ANY,ANY,ANY'
    x[i, j, ..., drop = FALSE]

    ## S4 method for signature 'TrioSetList,ANY,ANY'
    x[[i, j, ..., exact = TRUE]]

    ## S4 method for signature 'TrioSetList'
    show(object)

    ## S4 method for signature 'TrioSetList'
    length(x)

    ## S4 method for signature 'TrioSetList'
    x$name

    ## S4 method for signature 'TrioSetList,GRanges'
    MAP(object, ranges, id, TAUP = 1e+10,
      tauMAX = 1 - 5e-08, cnStates = c(-2, -0.4, 0, 0, 0.4, 1),
      pr.nonmendelian = 1.5e-06, mdThr = 0.9, ...)

    ## S4 method for signature 'TrioSetList'
    segment2(object, md = NULL, segmentParents = TRUE,
      verbose = TRUE, ...)

    ## S4 method for signature 'list'
    segment2(object, pos, chrom, id = NULL, featureNames,
      segmentParents = TRUE, verbose = TRUE, genome, ...)

### Arguments

`from` | a `TrioSetList`
`to` | a `RangedSummarizedExperiment`
`object` | a `TrioSetList` object
`x` | a `TrioSetList`
`i` | a numeric vector for subsetting the chromosomes (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.
`exact` | ignored
`name` | character string of a variable name in the phenoData
`ranges` | a `GRanges` object
`id` | a character vector of trio identifiers
`TAUP` | length-one numeric vector. Larger values decrease the probability of transitioning to an different state.
`tauMAX` | the maximum allowed transition probability
`cnStates` | a length-six numeric vector profiving initial values for the mean copy number for each of the 6 states
`pr.nonmendelian` | a length-one numeric vector indicating the probability of a non-Mendelian copy number alteration in the offspring
`mdThr` | a length-one numeric vector indicating the minimum value of the mean minimum distance. Segments with absolute mean value less than `mdThr` are not called.
`md` | a list of minimum distance matrices. Length of list should be the same as the length of the `TrioSetList` object.
`segmentParents` | logical. Whether to segment the parental log R ratios.
`verbose` | logical. Whether to display messages indicating progress.
`pos` | a list of the genomic positions (integers)
`chrom` | list of chromosome names
`featureNames` | a list of the marker names
`genome` | a character vector indicating the UCSC genome build used for the annotation (i.e., 'hg18' or 'hg19').

### Slots

`fatherPhenoData`

  `AnnotatedDataFrame` containing covariates for the father

`motherPhenoData`

  `AnnotatedDataFrame` containing covariates for the mother

`pedigree`

  an object of class `Pedigree`

[Package MinimumDistance version 1.28.0 Index]