FamilyExperiment-class: FamilyExperiment Class
In syounkin/Trioconductor: Trioconductor

The FamilyExperiment (FE) class is an extension of the SummarizedExperiment (SE) class defined in GenomicRanges. An FE object contains an additional slot for a pedigree object. If the FE object is designed to contain genotype data, then a SNPMatrix object named 'geno' must appear in the assayData list. Similarly with cnv data the assayData list must contain a matrix named 'cnv'.

In the following code snippets, fe is a FamilyExperiment object.

: pedigree(fe): Returns the pedigree object contained in fe. The returned object will have class PedClass.
: MAF(fe): Returns a numeric vector of minor allele frequencies. The frequencies are computed after subsetting the data to be parents only. This clearly is problematice if your pedigree contains multiple generations. This method is essentially a wrapper for the The minor allele frequency method of SnpStats.
: completeTrios(fe): Returns an n by 3 (character or factor)? matrix with rows that correspond to the parent-offspring trios contained in fe such that each of the trio members appears in the assay data. n is the number of “complete trios.”
: parents(fe): Returns the parents IDs. Note that this is intended to be used with parent-offspring trios. It will return any subject that has both parents in the pedigree data.
: baf(fe): Retrieve matrix of B allele frequencies. Not yet implemented.
: logr(fe): Retrieve matrix of log R ratio values. Not yet implemented.
: geno(fe): Retrieve a matrix of genotypes.
: cnv(fe):
: fe[i,j]: subset operator