snp.matrix-class {chopsticks} | R Documentation

## Class "snp.matrix"

### Description

This class defines objects holding large arrays of single nucleotide polymorphism (SNP) genotypes generated using array technologies.

### Objects from the Class

Objects can be created by calls of the form `new("snp.matrix", x)` where `x` is a matrix with storage mode `"raw"`. Chips (usually corresponding to samples or subjects) define rows of the matrix while polymorphisms (loci) define columns. Rows and columns will usually have names which can be used to link the data to further data concerning samples and SNPs

### Slots

`.Data`:

  Object of class `"matrix"` and storage mode `raw` Internally, missing data are coded `00` and SNP genotypes are coded `01`, `02` or `03`.

### Extends

Class `"matrix"`, from data part. Class `"structure"`, by class `"matrix"`. Class `"array"`, by class `"matrix"`. Class `"vector"`, by class "matrix", with explicit coerce. Class `"vector"`, by class "matrix", with explicit coerce.

### Methods

[]

  `signature(x = "snp.matrix")`: subset operations. Currently rather slow owing to excessive copying.

cbind2

  `signature(x = "snp.matrix", y = "snp.matrix")`: S4 generic function to provide cbind() for two or more matrices together by column. Row names must match and column names must not coincide. If the matrices are of the derived class `X.snp.matrix-class`, the `Female` slot values must also agree

coerce

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

coerce

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

coerce

  `signature(from = "matrix", to = "snp.matrix")`: maps numeric matrix (coded 0, 1, 2 or NA) to a snp.matrix

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`

is.na

  `signature(x = "snp.matrix")`: returns a logical matrix indicating whether each element is `NA`

rbind2

  `signature(x = "snp.matrix", y = "snp.matrix")`: S4 generic function to provide rbind() for two or more matrices by row. Column names must match and duplicated row names prompt warnings

show

  `signature(object = "snp.matrix")`: shows the size of the matrix (since most objects will be too large to show in full)

summary

  `signature(object = "snp.matrix")`: calculate call rates, allele frequencies, genotype frequencies, and z-tests for Hardy-Weinberg equilibrium. Results are returned as a dataframe with column names `Calls`, `Call.rate`, `MAF`, `P.AA`, `P.AB`, `P.BB`, and `z.HWE`

is.na

  `signature(x = "snp.matrix")`: returns a logical matrix of missing call indicators

show

  `signature(object = "snp.matrix")`: ...

summary

  `signature(object = "snp.matrix")`: ...

### Note

This class requires at least version 2.3 of R

### Author(s)

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

### References

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

### See Also

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

### Examples

    data(testdata)
    summary(summary(Autosomes))

    # Just making it up - 3-10 will be made into NA during conversion
    snps.class<-new("snp.matrix", matrix(1:10))
    snps.class
    if(!isS4(snps.class)) stop("constructor is not working")

    pretend.X <- as(Autosomes, 'X.snp.matrix')
    if(!isS4(pretend.X)) stop("coersion to derived class is not S4")
    if(class(pretend.X) != 'X.snp.matrix') stop("coersion to derived class is not working")

    pretend.A <- as(Xchromosome, 'snp.matrix')
    if(!isS4(pretend.A)) stop("coersion to base class is not S4")
    if(class(pretend.A) != 'snp.matrix') stop("coersion to base class is not working")

[Package chopsticks version 1.56.0 Index]