Routines for reading and manipulating GWAS data in .bed files
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Data from Genome-wide association studies
are often saved as a PLINK binary biallelic genotype table
or .bed file.
To be useful, such files should be accompanied by a .fam file, containing metadata on the rows of the table, and a .bim file,
containing metadata on the columns.
The .fam and .bim files are in tab-separated format.
The table contains the observed allelic type at n
single-nucleotide polymorphism (SNP) positions
for m individuals.
A SNP corresponds to a nucleotide position on the genome where some degree of variation has been observed in a population,
with each individual have one of two possible alleles at that position on each of a pair of chromosomes.
Three possible types can be observed are:
homozygous allele 1, coded as 0x00, heterzygous, coded as 0x10, and homozygous allele 2, coded as 0x11.
Missing values are coded as 0x01.
A single column - one SNP position over all m individuals - is packed into an
array of div(m + 3, 4) bytes (UInt8 values).
This package requires Julia v0.7.0 or later, which can be obtained from https://julialang.org/downloads/ or by building Julia from the sources in the https://github.com/JuliaLang/julia repository.
The package has not yet been registered and must be installed using the repository location.
Start julia and use the ] key to switch to the package manager REPL
(v0.7) pkg> add https://github.com/dmbates/BEDFiles.jl.git#master
Updating git-repo `https://github.com/dmbates/BEDFiles.jl.git`
Updating registry at `~/.julia/registries/Uncurated`
Updating git-repo `https://github.com/JuliaRegistries/Uncurated.git`
Resolving package versions...
Updating `~/.julia/environments/v0.7/Project.toml`
[6f44c9a6] + BEDFiles v0.1.0 #master (https://github.com/dmbates/BEDFiles.jl.git)
Updating `~/.julia/environments/v0.7/Manifest.toml`
[6f44c9a6] + BEDFiles v0.1.0 #master (https://github.com/dmbates/BEDFiles.jl.git)
[6fe1bfb0] + OffsetArrays v0.6.0
[10745b16] + Statistics Use the backspace key to return to the Julia REPL.
Please see the documentation