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

In rscharpf/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 '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, ...)

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

rscharpf/MinimumDistance documentation built on Sept. 16, 2019, 4:12 a.m.