R: A Suite of Packages for Analysis of Big Genomic Data

# A Suite of Packages for Analysis of Big Genomic Data

## Documentation for package ‘BGData’ version 2.4.1

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

BGData-package | A Suite of Packages for Analysis of Big Genomic Data
as.BGData | Convert Other Objects to BGData Objects
as.BGData.BEDMatrix | Convert Other Objects to BGData Objects
as.BGData.ColumnLinkedMatrix | Convert Other Objects to BGData Objects
as.BGData.RowLinkedMatrix | Convert Other Objects to BGData Objects
BGData | Creates a New BGData Instance
BGData-class | Container for Phenotype and Genotype Data
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
findRelated.matrix | Find related individuals in a relationship matrix
findRelated.symDMatrix | Find related individuals in a relationship matrix
FWD | Performs Forward Regressions
geno | Getting/Setting Genotypes, Sample Information, and Variant Information
geno-class | An Abstract S4 Class Union of Matrix-Like Types
geno-method | Container for Phenotype and Genotype Data
geno<- | Getting/Setting Genotypes, Sample Information, and Variant Information
geno<--method | Container for Phenotype and Genotype Data
getG | Computes a Genomic Relationship Matrix
getG_symDMatrix | Computes a Very Large Genomic Relationship Matrix
GWAS | Performs Single Marker Regressions Using BGData Objects
load.BGData | Loads BGData (and Other) Objects from .RData Files
map | Getting/Setting Genotypes, Sample Information, and Variant Information
map-method | Container for Phenotype and Genotype Data
map<- | Getting/Setting Genotypes, Sample Information, and Variant Information
map<--method | Container for Phenotype and Genotype Data
multi-level-parallelism | Multi-Level Parallelism
orderedMerge | Merge Two Data Frames Keeping the Order of the First
pheno | Getting/Setting Genotypes, Sample Information, and Variant Information
pheno-method | Container for Phenotype and Genotype Data
pheno<- | Getting/Setting Genotypes, Sample Information, and Variant Information
pheno<--method | Container for Phenotype and Genotype Data
preprocess | Center, scale, and impute data
readRAW | Creates a BGData Object From a .raw File or a .ped-Like File
readRAW_big.matrix | Creates a BGData Object From a .raw File or a .ped-Like File
readRAW_matrix | Creates a BGData Object From a .raw File or a .ped-Like File
segments | Find non-overlapping segments based on a summary statistic
summarize | Generates Various Summary Statistics