TrioSet-class: Deprecated class for storing low-level genomic data for trios

In MinimumDistance: A Package for De Novo CNV Detection in Case-Parent 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

MinimumDistance documentation built on Nov. 8, 2020, 11:11 p.m.