R Functions Reference

1 Overview

Complete reference for all R functions in BigDataStatMeth v2. The package provides two layers of functionality: a primary S3 interface based on HDF5Matrix objects that integrates with standard R generics, and a set of legacy bd* functions retained for compatibility and specialized use.

2 New S3 Interface

2.1 HDF5Matrix Core

Create, open, inspect and manage HDF5Matrix objects.

2.2 Decompositions & Factorizations

SVD, PCA, QR, Cholesky, eigen, solve and pseudoinverse on HDF5Matrix objects.

2.3 Aggregations & Statistics

Column/row summaries, correlation, normalization, and apply operations.

2.4 Matrix Utilities

Diagonal operations and sparse matrix multiplication.

2.5 Omics QC & Preprocessing

SNP imputation, missingness filtering, and MAF filtering.

3 Legacy bd* Interface

3.1 In-Memory Linear Algebra

Block multiplication, crossproduct, pseudoinverse and correlation on R matrices.

3.2 HDF5 I/O & Management

Low-level HDF5 dataset and group management utilities.

4 Utilities

4.1 System & Memory Utilities

RAM, CPU, and thread information for capacity planning.