X.snp-class {chopsticks}

R Documentation

Class "X.snp"

Description

Compact representation of data concerning single nucleotide polymorphisms (SNPs) on the X chromosome

Objects from the Class

Objects can be created by calls of the form new("snp", ..., Female=...) or by subset selection from an object of class "X.snp.matrix". Holds one row or column of an object of class "X.snp.matrix"

Slots

.Data:

The genotype data coded as 0, 1, 2, or 3. For males are coded as homozygious females

Female:

A logical array giving the sex of the sample(s)

Extends

Class "snp", directly. Class "raw", by class "snp". Class "vector", by class "snp".

Methods

coerce

signature(from = "X.snp", to = "character"): map to codes "A/A", "A/B", "B/B", "A/Y", "B/Y", or ""

coerce

signature(from = "X.snp", to = "numeric"): map to codes 0, 1, 2, or NA

coerce

signature(from = "X.snp", to = "genotype"): Yet to be implemented

show

signature(object = "X.snp"): shows character representation of the object

Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

References

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

See Also

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

Examples

data(testdata)
s <- Xchromosome[,1]
class(s)
s

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