R: Formal class "SNPbin"

SNPbin-class {adegenet} | R Documentation

## Formal class "SNPbin"

### Description

The class `SNPbin` is a formal (S4) class for storing a genotype of binary SNPs in a compact way, using a bit-level coding scheme. This storage is most efficient with haploid data, where the memory taken to represent data can reduced more than 50 times. However, `SNPbin` can be used for any level of ploidy, and still remain an efficient storage mode.

A `SNPbin` object can be constructed from a vector of integers giving the number of the second allele for each locus.

`SNPbin` stores a single genotype. To store multiple genotypes, use the genlight class.

### Objects from the class SNPbin

`SNPbin` objects can be created by calls to `new("SNPbin", ...)`, where '...' can be the following arguments:

`snp`

  a vector of integers or numeric giving numbers of copies of the second alleles for each locus. If only one unnamed argument is provided to 'new', it is considered as this one.

`ploidy`

  an integer indicating the ploidy of the genotype; if not provided, will be guessed from the data (as the maximum from the 'snp' input vector).

`label`

  an optional character string serving as a label for the genotype.

### Slots

The following slots are the content of instances of the class `SNPbin`; note that in most cases, it is better to retrieve information via accessors (see below), rather than by accessing the slots manually.

`snp`:

  a list of vectors with the class `raw`.

`n.loc`:

  an integer indicating the number of SNPs of the genotype.

`NA.posi`:

  a vector of integer giving the position of missing data.

`label`:

  an optional character string serving as a label for the genotype..

`ploidy`:

  an integer indicating the ploidy of the genotype.

### Methods

Here is a list of methods available for `SNPbin` objects. Most of these methods are accessors, that is, functions which are used to retrieve the content of the object. Specific manpages can exist for accessors with more than one argument. These are indicated by a '*' symbol next to the method's name. This list also contains methods for conversion from `SNPbin` to other classes.

[

  `signature(x = "SNPbin")`: usual method to subset objects in R. The argument indicates how SNPs are to be subsetted. It can be a vector of signed integers or of logicals.

show

  `signature(x = "SNPbin")`: printing of the object.

$

  `signature(x = "SNPbin")`: similar to the @ operator; used to access the content of slots of the object.

$<-

  `signature(x = "SNPbin")`: similar to the @ operator; used to replace the content of slots of the object.

nLoc

  `signature(x = "SNPbin")`: returns the number of SNPs in the object.

names

  `signature(x = "SNPbin")`: returns the names of the slots of the object.

ploidy

  `signature(x = "SNPbin")`: returns the ploidy of the genotype.

as.integer

  `signature(x = "SNPbin")`: converts a `SNPbin` object to a vector of integers. The S4 method 'as' can be used as well (e.g. as(x, "integer")).

cbind

  `signature(x = "SNPbin")`: merges genotyping of the same individual at different SNPs (all stored as SNPbin objects) into a single SNPbin.

c

  `signature(x = "SNPbin")`: same as cbind.SNPbin.

### Author(s)

Thibaut Jombart (t.jombart@imperial.ac.uk)

### See Also

Related class:
- `genlight`, for storing multiple binary SNP genotypes.
- `genind`, for storing other types of genetic markers.

### Examples

    ## Not run:
    #### HAPLOID EXAMPLE ####
    ## create a genotype of 100,000 SNPs
    dat <- sample(c(0,1,NA), 1e5, prob=c(.495, .495, .01), replace=TRUE)
    dat[1:10]
    x <- new("SNPbin", dat)
    x
    x[1:10] # subsetting
    as.integer(x[1:10])

    ## try a few accessors
    ploidy(x)
    nLoc(x)
    head(x$snp[[1]]) # internal bit-level coding

    ## check that conversion is OK
    identical(as(x, "integer"),as.integer(dat)) # SHOULD BE TRUE

    ## compare the size of the objects
    print(object.size(dat), unit="auto")
    print(object.size(x), unit="auto")
    object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION

    #### TETRAPLOID EXAMPLE ####
    ## create a genotype of 100,000 SNPs
    dat <- sample(c(0:4,NA), 1e5, prob=c(rep(.995/5,5), 0.005), replace=TRUE)
    x <- new("SNPbin", dat)
    identical(as(x, "integer"),as.integer(dat)) # MUST BE TRUE

    ## compare the size of the objects
    print(object.size(dat), unit="auto")
    print(object.size(x), unit="auto")
    object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION

    #### c, cbind ####
    a <- new("SNPbin", c(1,1,1,1,1))
    b <- new("SNPbin", c(0,0,0,0,0))
    a
    b
    ab <- c(a,b)
    ab
    identical(c(a,b),cbind(a,b))
    as.integer(ab)

    ## End(Not run)

[Package adegenet version 2.1.4 Index]