R: Reading Single Nucleotide Polymorphism data

read.snp {adegenet} | R Documentation

## Reading Single Nucleotide Polymorphism data

### Description

The function `read.snp` reads a SNP data file with extension '.snp' and converts it into a genlight object. This format is devoted to handle biallelic SNP only, but can accommodate massive datasets such as complete genomes with considerably less memory than other formats.

### Usage

    read.snp(
      file,
      quiet = FALSE,
      chunkSize = 1000,
      parallel = FALSE,
      n.cores = NULL,
      ...
    )

### Arguments

`file` | a character string giving the path to the file to convert, with the extension ".snp".
`quiet` | logical stating whether a conversion messages should be printed (TRUE,default) or not (FALSE).
`chunkSize` | an integer indicating the number of genomes to be read at a time; larger values require more RAM but decrease the time needed to read the data.
`parallel` | a logical indicating whether multiple cores -if available- should be used for the computations (TRUE, default), or not (FALSE); requires the package `parallel` to be installed (see details).
`n.cores` | if `parallel` is TRUE, the number of cores to be used in the computations; if NULL, then the maximum number of cores available on the computer is used.
`...` | other arguments to be passed to other functions - currently not used.

### Details

The function reads data by chunks of a few genomes (minimum 1, no maximum) at a time, which allows one to read massive datasets with negligible RAM requirements (albeit at a cost of computational time). The argument `chunkSize` indicates the number of genomes read at a time. Increasing this value decreases the computational time required to read data in, while increasing memory requirements.

A description of the .snp format is provided in an example file distributed with adegenet (see example below).

=== The .snp format ===

Details of the .snp format can be found in the example file distributed with adegenet (see below), or on the adegenet website (type `adegenetWeb()` in R).

### Value

an object of the class `"genlight"`

### Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

### See Also

- `?genlight` for a description of the class `"genlight"`.

- `read.PLINK`: read SNPs in PLINK's '.raw' format.

- `fasta2genlight`: extract SNPs from alignments with fasta format.

- `df2genind`: convert any multiallelic markers into adegenet `"genlight"`.

- `import2genind`: read multiallelic markers from various software into adegenet.

### Examples

    ## Not run:
    ## show the example file ##
    ## this is the path to the file:
    system.file("files/exampleSnpDat.snp",package="adegenet")

    ## show its content:
    file.show(system.file("files/exampleSnpDat.snp",package="adegenet"))

    ## read the file
    obj <-
    read.snp(system.file("files/exampleSnpDat.snp",package="adegenet"), chunk=2)
    obj
    as.matrix(obj)
    ploidy(obj)
    alleles(obj)
    locNames(obj)

    ## End(Not run)

[Package adegenet version 2.1.4 Index]