read.PLINK: Reading PLINK Single Nucleotide Polymorphism data

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Reading PLINK Single Nucleotide Polymorphism data

Description

The function read.PLINK reads a data file exported by the PLINK software with extension '.raw' and converts it into a "genlight" object. Optionally, information about SNPs can be read from a ".map" file, either by specifying the argument map.file in read.PLINK, or using extract.PLINKmap to add information to an existing "genlight" object.

Usage

extract.PLINKmap(file, x = NULL)

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

Arguments

file	for read.PLINK a character string giving the path to the file to convert, with the extension ".raw"; for extract.PLINKmap, a character string giving the path to a file with extension ".map".
x	an optional object of the class "genlight", in which the information read is stored; if provided, information is matched against the names of the loci in x, as returned by locNames(x); if not provided, a list of two components is returned, containing chromosome and position information.
map.file	an optional character string indicating the path to a ".map" file, which contains information about the SNPs (chromosome, position). If provided, this information is processed by extract.PLINKmap and stored in the @other slot.
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 several 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.

See details for the documentation about how to export data using PLINK to the '.raw' format.

=== Exporting data from PLINK ===

Data need to be exported from PLINK using the option "–recodeA" (and NOT "–recodeAD"). The PLINK command should therefore look like: plink --file data --recodeA. For more information on this topic, please look at this webpage: http://zzz.bwh.harvard.edu/plink/

Value

- read.PLINK: an object of the class "genlight"

- extract.PLINKmap: if a "genlight" is provided as argument x, this object incorporating the new information about SNPs in the @other slot (with new components 'chromosome' and 'position'); otherwise, a list with two components containing chromosome and position information.

Author(s)

Thibaut Jombart [e-mail]

See Also

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

- read.snp: read SNPs in adegenet's '.snp' format.

- fasta2genlight: extract SNPs from alignments with fasta format.

- other import function in adegenet: import2genind, df2genind, read.genetix read.fstat, read.structure, read.genepop.

- another function read.plink is available in the package snpMatrix.

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