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MinimumDistance (version 1.16.0)

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

Description

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

Usage

"pedigree"(object)


"show"(object)


"mindist"(object)


"mindist"(object) <- value


"dim"(x)


"trios"(object)


"["(x, i, j, ..., drop = FALSE)


"MAP"(object, ranges, transition_param = TransitionParam(), emission_param = EmissionParam(), mdThr = 0.9, ...)


"["(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