X.snp.matrix-class {snpMatrix}R Documentation

Class "X.snp.matrix"

Description

This class extends the snp.matrix-class to deal with SNPs on the X chromosome.

Objects from the Class

Objects can be created by calls of the form new("X.snp.matrix", x, Female). Such objects have an additional slot to objects of class "snp.matrix" consisting of a logical array of the same length as the number of rows. This array indicates whether the sample corresponding to that row came from a female (TRUE) or a male (FALSE).

Slots

.Data:
Object of class "matrix" and storage mode "raw"
Female:
Object of class "logical" indicating sex of samples

Extends

Class "snp.matrix", directly, with explicit coerce. Class "matrix", by class "snp.matrix". Class "structure", by class "snp.matrix". Class "array", by class "snp.matrix". Class "vector", by class "snp.matrix", with explicit coerce. Class "vector", by class "snp.matrix", with explicit coerce.

Methods

[
signature(x = "X.snp.matrix"): subset operations
[<-
signature(x = "X.snp.matrix"): subset assignment operation to replace part of an object
coerce
signature(from = "X.snp.matrix", to = "character"): map to codes 0, 1, 2, or NA
coerce
signature(from = "snp.matrix", to = "X.snp.matrix"): maps a snp.matrix to an X.snp.matrix. Sex is inferred from the genotype data since males should not be heterozygous at any locus. After inferring sex, heterozygous calls for males are set to NA
show
signature(object = "X.snp.matrix"): map to codes "A/A", "A/B", "B/B", "A/Y", "B/Y" or ""
summary
signature(object = "X.snp.matrix"): returns the sex distribution, together with summaries of the data frames returned by row.summary and col.summary

Author(s)

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

References

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

See Also

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

Examples

data(testdata)
summary(Xchromosome)

[Package snpMatrix version 1.8.0 Index]