chopsticks (version 1.36.0)

X.snp.matrix-class: 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. Currently rather slow owing to excessive copying

[<-

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"): calculate call rates, allele frequencies, genotype frequencies, and chi-square tests for Hardy-Weinberg equilibrium. Genotype frequencies are calculated for males and females separately and Hardy-Weinberg equilibrium tests use only the female data. Allele frequencies are calculated using data from both males and females. Results are returned as a dataframe with column names Calls, Call.rate, MAF, P.AA, P.AB, P.BB, P.AY, P.BY, and z.HWE

References

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

See Also

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

Examples

data(testdata)
summary(summary(Xchromosome))