gl2plink {dartR}

Converts a genlight object into PLINK format

Description

This function exports a genlight object into PLINK format and save it into a file. This function produces the following PLINK files: bed, bim, fam, ped and map.

Usage

gl2plink(
  x,
  plink_path = getwd(),
  bed_file = FALSE,
  outfile = "gl_plink",
  outpath = tempdir(),
  chr_format = "character",
  pos_cM = "0",
  ID_dad = "0",
  ID_mom = "0",
  sex_code = "unknown",
  phen_value = "0",
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP data [required].

plink_path

Path of PLINK binary file [default getwd()].

bed_file

Whether create PLINK files .bed, .bim and .fam [default FALSE].

outfile

File name of the output file [default 'gl_plink'].

outpath

Path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory.

chr_format

Whether chromosome information is stored as 'numeric' or as 'character', see details [default 'character'].

pos_cM

A vector, with as many elements as there are loci, containing the SNP position in morgans or centimorgans [default '0'].

ID_dad

A vector, with as many elements as there are individuals, containing the ID of the father, '0' if father isn't in dataset [default '0'].

ID_mom

A vector, with as many elements as there are individuals, containing the ID of the mother, '0' if mother isn't in dataset [default '0'].

sex_code

A vector, with as many elements as there are individuals, containing the sex code ('male', 'female', 'unknown'). Sex information needs just to start with an "F" or "f" for females, with an "M" or "m" for males and with a "U", "u" or being empty if the sex is unknown [default 'unknown'].

phen_value

A vector, with as many elements as there are individuals, containing the phenotype value. '1' = control, '2' = case, '0' = unknown [default '0'].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

To create PLINK files .bed, .bim and .fam (bed_file = TRUE), it is necessary to download the binary file of PLINK 1.9 and provide its path (plink_path). The binary file can be downloaded from: https://www.cog-genomics.org/plink/

After downloading, unzip the file, access the unzipped folder and move the binary file ("plink") to your working directory.

If you are using a Mac, you might need to open the binary first to grant access to the binary.

The chromosome of each SNP can be a character or numeric. The chromosome information for unmapped SNPS is coded as 0. Family ID is taken from x$pop. Within-family ID (cannot be '0') is taken from indNames(x). Variant identifier is taken from locNames(x). SNP position is taken from the accessor x$position. Chromosome name is taken from the accessor x$chromosome Note that if names of populations or individuals contain spaces, they are replaced by an underscore "_".

If you like to use chromosome information when converting to plink format and your chromosome names are not from human, you need to change the chromosome names as 'contig1', 'contig2', etc. as described in the section "Nonstandard chromosome IDs" in the following link: https://www.cog-genomics.org/plink/1.9/input

Note that the function might not work if there are spaces in the path to the plink executable.

Value

returns no value (i.e. NULL)

Author(s)

Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

References

Purcell, Shaun, et al. 'PLINK: a tool set for whole-genome association and population-based linkage analyses.' The American journal of human genetics 81.3 (2007): 559-575.

Examples

require("dartR.data")
test <- platypus.gl
# assigning SNP position
test$position <- test$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1
# assigning a dummy name for chromosomes
test$chromosome <- as.factor("1")
gl2plink(test)