This class is inspired by the phenotype/genotype file format .raw and its
binary companion (also known as .bed) of
PLINK. It is used by several
functions of this package such as
GWAS() for performing a Genome Wide
Association Study or
getG() for calculating a genomic relationship matrix.
There are several ways to create an instance of this class:
from arbitrary phenotype/genotype data using one of the constructors
from a BED file using
from a previously saved BGData object using
from multiple files (even a mixture of different file types) using LinkedMatrix::LinkedMatrix.
from a .raw file (or a .ped-like file) using
A .ped file can be recoded to a .raw file in
plink --file myfile --recodeA, or converted to a BED file using
plink --file myfile --make-bed. Conversely, a BED file can be transformed back to a .ped file
plink --bfile myfile --recode or to a .raw file using
plink --bfile myfile --recodeA without losing information.
A geno object that contains genotypes. geno is a
class union of several matrix-like types, many of them suitable for very
large datasets. Currently supported are LinkedMatrix::LinkedMatrix,
data.frame that contains phenotypes.
data.frame that contains a genetic map.
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