adegenet (version 2.0.0)

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 = require("parallel"), 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.

Value

• an object of the class "genlight"

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).

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

## 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)