Learn R Programming
MinimumDistance (version 1.16.0)

TrioSetList-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

"coerce"(from, to)


"pedigree"(object)


"trios"(object)


"offspringNames"(object)


"["(x, i, j, ..., drop = FALSE)


"[["(x, i, j, ..., exact = TRUE)


"show"(object)


"length"(x)


"$"(x, name)


"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, ...)


"segment2"(object, md = NULL, segmentParents = TRUE, verbose = TRUE, ...)


"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