A Suite of Packages for Analysis of Big Genomic Data

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Documentation for package ‘BGData’ version 2.4.1

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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