XSnpMatrix-class {snpStats} | R Documentation

## Class "XSnpMatrix"

### Description

This class extends the `SnpMatrix-class` to deal with SNPs on the X and Y chromosomes and mitocondrial SNPs.

### Objects from the Class

Objects can be created by calls of the form `new("XSnpMatrix", x, diploid)`. Such objects have an additional `slot` to objects of class `"SnpMatrix"` consisting of a logical array of the same length as the number of rows. This array indicates whether genotypes in that row are diploid (`TRUE`) or haploid (`FALSE` as, for example, SNPs on the X chromosome for males).

### Slots

`.Data`:

  Object of class `"matrix"` and storage mode `"raw"`

`diploid`:

  Object of class `"logical"` indicating sex of samples

### Extends

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

### Methods

[]

  `signature(x = "XSnpMatrix", i = "ANY", j = "ANY", drop = "missing")`: subset extraction

[<-

  `signature(x = "XSnpMatrix", i = "ANY", j = "ANY", "XSnpMatrix")`: subset assignment operation to replace part of an object

coerce

  `signature(from = "XSnpMatrix", to = "character")`: map to codes 0, 1, 2, or NA

coerce

  `signature(from = "SnpMatrix", to = "XSnpMatrix")`: maps a SnpMatrix to an XSnpMatrix. Ploidy is inferred from the genotype data since haploid genotypes should always be coded as homozygous. After inferring ploidy, heterozygous calls for haploid genotpes are set to `NA`

show

  `signature(object = "XSnpMatrix")`: map to codes "A/A", "A/B", "B/B", "A", "B" or ""

summary

  `signature(object = "XSnpMatrix")`: returns the distribution of ploidy, together with summaries of the data frames returned by `row.summary` and `col.summary`

### Author(s)

David Clayton dc208@cam.ac.uk

### See Also

`SnpMatrix-class`

### Examples

    data(testdata)
    summary(Xchromosome)

    # display the first 10 snps of the first 10 samples
    print(as(Xchromosome[1:10,1:10],'character'))

    # convert the empty strings (no-calls) explicitly to "NC" before
    # writing to an (anonymous and temporary) csv file
    csvfile <- tempfile()
    write.csv(file=csvfile, gsub ('^$', 'NC',
                                  as(Xchromosome[1:10,1:10], 'character')
                                 ), quote=FALSE)
    unlink(csvfile)

[Package snpStats version 1.40.0 Index]