snpMatrix (version 1.19.24)

snp.matrix-class: Class "snp.matrix"

Description

This class defines objects holding large arrays of single nucleotide polymorphism (SNP) genotypes generated using array technologies.

Objects from the Class

Objects can be created by calls of the form new("snp.matrix", x) where x is a matrix with storage mode "raw". Chips (usually corresponding to samples or subjects) define rows of the matrix while polymorphisms (loci) define columns. Rows and columns will usually have names which can be used to link the data to further data concerning samples and SNPs

Extends

Class "matrix", from data part. Class "structure", by class "matrix". Class "array", by class "matrix". Class "vector", by class "matrix", with explicit coerce. Class "vector", by class "matrix", with explicit coerce.

References

http://www-gene.cimr.cam.ac.uk/clayton

See Also

snp-class, X.snp-class, X.snp.matrix-class

Examples

data(testdata)
summary(summary(Autosomes))

# Just making it up - 3-10 will be made into NA during conversion
snps.class<-new("snp.matrix", matrix(1:10))
snps.class
if(!isS4(snps.class)) stop("constructor is not working")

pretend.X <- as(Autosomes, 'X.snp.matrix')
if(!isS4(pretend.X)) stop("coersion to derived class is not S4")
if(class(pretend.X) != 'X.snp.matrix') stop("coersion to derived class is not working")

pretend.A <- as(Xchromosome, 'snp.matrix')
if(!isS4(pretend.A)) stop("coersion to base class is not S4")
if(class(pretend.A) != 'snp.matrix') stop("coersion to base class is not working")