TrioSet-class {MinimumDistance} | R Documentation |
This class is deprecated and will be defunct in a future release.
## 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]
object |
a |
value |
a |
x |
a |
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 |
transition_param |
an object of class |
emission_param |
an object of class |
mdThr |
the minimum absolute value of the minimum distance
segment mean. Segments with means below |
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