read.snp: Reading Single Nucleotide Polymorphism data

In adegenet: Exploratory Analysis of Genetic and Genomic Data

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 [e-mail]

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)

adegenet documentation built on Feb. 16, 2023, 6 p.m.