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

Description Usage Arguments Slots

Description

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

Usage

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## 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


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