Description Usage Arguments Slots

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 | ```
## 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,
...
)
``` |

`from` |
a |

`to` |
a |

`object` |
a |

`x` |
a |

`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 |

`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 |

`md` |
a list of minimum distance matrices. Length of list
should be the same as the length of the |

`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'). |

`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.

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