TrioSetList-class: Deprecated class for storing low-level genomic data for trios
In MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

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

## 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,
  ...
)

`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').

fatherPhenoData: AnnotatedDataFrame containing covariates for the father
motherPhenoData: AnnotatedDataFrame containing covariates for the mother
pedigree: an object of class Pedigree