Container for Phenotype and Genotype Data
The BGData class is a container for genotypes, sample information, and
variant information. The class is inspired by the .bed/.fam/.bim
(binary) and .ped/.fam/.map (text) phenotype/genotype file formats
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 the BGData
constructor function.
from a .bed file using as.BGData and BEDMatrix.
from a previously saved BGData object using
load.BGData.
from multiple files (even a mixture of different file types)
using LinkedMatrix.
from a .raw file (or a .ped-like file) using
readRAW, readRAW_matrix, or
readRAW_big.matrix.
A .ped file can be recoded to a .raw file in
PLINK using 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 using plink --bfile myfile --recode or to a .raw file
using plink --bfile myfile --recodeA without losing information.
In the following code snippets, x is a BGData object.
geno(x), geno(x) <- value:Get or set genotypes.
pheno(x), pheno(x) <- value:Get or set sample information.
map(x), map(x) <- value:Get or set variant information.
BGData, as.BGData, load.BGData,
readRAW to create BGData objects.
LinkedMatrix-class and
BEDMatrix-class for more information on the above
mentioned classes.
X <- matrix(data = rnorm(100), nrow = 10, ncol = 10) Y <- data.frame(y = runif(10)) MAP <- data.frame(means = colMeans(X), freqNA = colMeans(is.na(X))) DATA <- BGData(geno = X, pheno = Y, map = MAP) dim(geno(DATA)) head(pheno(DATA)) head(map(DATA))
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