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

[Package chopsticks version 1.52.0 Index]