snp-class: Class "snp"

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Description

Compact representation of data concerning single nucleotide polymorphisms (SNPs)

Objects from the Class

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

Slots

.Data:

The genotype data coded as 0, 1, 2, or 3

Methods

coerce

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

coerce

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

coerce

signature(from = "snp", to = "genotype"): maps a single SNP to an object of class "genotype". See the "genetics" package

.

show

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

is.na

signature(x = "snp"): returns a logical vector of missing call indicators

Author(s)

David Clayton [e-mail]

References

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

See Also

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

Examples

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

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.