TrioSetList-class {MinimumDistance} | R Documentation |
This class is deprecated and will be defunct in a future release.
## 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