BGData-class: Container for Phenotype and Genotype Data
In QuantGen/BGData: A Suite of Packages for Analysis of Big Genomic Data

BGData-class

R Documentation

Container for Phenotype and Genotype Data

Description

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.

Details

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.

Accessors

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.

Examples

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))

QuantGen/BGData documentation built on Jan. 21, 2025, 7:51 a.m.