A Suite of Packages for Analysis of Big Genomic Data


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Documentation for package ‘BGData’ version 2.1.0

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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 An S4 Class to Represent Phenotype and Genotype Data.
BGData-class An S4 Class to Represent 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.
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.
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.
GWAS Performs Single Marker Regressions Using BGData Objects.
initialize-method Creates a New BGData Instance.
load.BGData Loads BGData (and Other) Objects from .RData Files.
orderedMerge Merge Two Data Frames Keeping the Order of the First
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.
summarize Generates Various Summary Statistics.