adegenet: read.snp – R documentation

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read.snp

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

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)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release