MinimumDistance (version 1.16.0)

TrioSet: Deprecated constructor for TrioSet class

Description

The TrioSet class has been deprecated and may be removed in a future release.

Usage

TrioSet(pedigreeData = Pedigree(), sample.sheet, row.names = NULL, lrr, baf, featureData, cdfname, drop = TRUE, mindist = NULL, genome = c("hg19", "hg18"))

Arguments

pedigreeData

an object of class Pedigree

sample.sheet

a data.frame containing metadata on the trios

row.names

a character vector providing row identifiers for the sample.sheet argument that match the names of the trios in the pedigreeData argument.

lrr

a matrix of log R ratios

baf

a matrix of B allele frequencies

featureData

a GenomeAnnotatedDataFrame object for the SNPs/nonpolymorphic markers

cdfname

character string indicating the annotation package used to extract physical position and chromosome of markers

drop

logical. When FALSE, the dimnames on the log R ratio and BAF arrays is set to NULL

mindist

can be either NULL or a matrix of the minimum distance

genome

character string providing the UCSC genome build

Value

TrioSet

Examples

	path <- system.file("extdata", package="MinimumDistance")
	load(file.path(path, "logRratio.rda"))
	load(file.path(path, "baf.rda"))
	load(file.path(path, "pedigreeInfo.rda"))
	trioSet <- TrioSet(lrr=logRratio,
			   baf=baf,
			   pedigree=Pedigree(pedigreeInfo),
			   cdfname="human610quadv1bCrlmm",
			   genome="hg18")