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BGData

A Suite of Packages for Analysis of Big Genomic Data

An umbrella package providing a phenotype/genotype data structure and scalable and efficient computational methods for large genomic datasets in combination with several other packages: 'BEDMatrix', 'LinkedMatrix', and 'symDMatrix'.

Functions (19)

BGData

Creates a New BGData Instance

BGData-class

Container for Phenotype and Genotype Data

BGData-package

A Suite of Packages for Analysis of Big Genomic Data

GWAS

Performs Single Marker Regressions Using BGData Objects

as.BGData

Convert Other Objects to BGData Objects

chunkedApply

Applies a Function on Each Row or Column of a File-Backed Matrix

chunkedMap

Applies a Function on Each Chunk of a File-Backed Matrix

file-backed-matrices

File-Backed Matrices

findRelated

Find related individuals in a relationship matrix

geno

Getting/Setting Genotypes, Sample Information, and Variant Information

geno-class

An Abstract S4 Class Union of Matrix-Like Types

getG

Computes a Genomic Relationship Matrix

getG_symDMatrix

Computes a Very Large Genomic Relationship Matrix

load.BGData

Loads BGData (and Other) Objects from .RData Files

multi-level-parallelism

Multi-Level Parallelism

orderedMerge

Merge Two Data Frames Keeping the Order of the First

preprocess

Center, scale, and impute data

readRAW

Creates a BGData Object From a .raw File or a .ped-Like File

summarize

Generates Various Summary Statistics

BGData

A Suite of Packages for Analysis of Big Genomic Data

v2.2.0

MIT + file LICENSE

Authors

Gustavo de los Campos [aut], Alexander Grueneberg [aut, cre], Paulino Perez [ctb], Ana Vazquez [ctb]

Initial release

BGData

Functions (19)

BGData

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