Title: Scalable Statistical Computing with HDF5-Backed Matrices

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Documentation for package ‘BigDataStatMeth’ version 2.0.0

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

A B C D E F G H I L M O P Q R S T V misc

-- A --

apply_function	Apply a statistical or algebraic function to HDF5 datasets (generic)
as.data.frame.HDF5Matrix	Convert HDF5Matrix to data.frame
as.matrix.HDF5Matrix	Convert HDF5Matrix to in-memory matrix

-- B --

bdapply_Function_hdf5	Apply function to different datasets inside a group
bdblockMult	Block-Based Matrix Multiplication
bdblockSubstract	Block-Based Matrix Subtraction
bdblockSum	Block-Based Matrix Addition
bdCorr_matrix	Compute correlation matrix for in-memory matrices (unified function)
bdCreate_hdf5_group	Create Group in an HDF5 File
bdCreate_hdf5_matrix	Create HDF5 data file and write data to it
bdCrossprod	Efficient Matrix Cross-Product Computation
bdgetDatasetsList_hdf5	List Datasets in HDF5 Group
bdImportData_hdf5	Import data from URL or file to HDF5 format
bdImportTextFile_hdf5	Import Text File to HDF5
bdmove_hdf5_dataset	Move HDF5 Dataset
bdpseudoinv	Compute Matrix Pseudoinverse (In-Memory)
bdpseudoinv_hdf5	Compute Matrix Pseudoinverse (HDF5-Stored)
bdReduce_hdf5_dataset	Reduce Multiple HDF5 Datasets
bdScalarwproduct	Matrix–scalar weighted product
bdtCrossprod	Efficient Matrix Transposed Cross-Product Computation
bdWrite_hdf5_dimnames	Write dimnames to an HDF5 dataset
bd_wproduct	Weighted matrix–vector products and cross-products
BigDataStatMeth	BigDataStatMeth: Scalable statistical computing with R, C++, and HDF5

-- C --

cancer	Cancer classification
can_allocate	Check if memory allocation is safe
cbind.HDF5Matrix	Column-bind HDF5Matrix objects
chol.HDF5Matrix	Cholesky decomposition of a symmetric positive-definite HDF5Matrix
close.HDF5Matrix	Close HDF5Matrix
colesterol	Dataset colesterol
colMaxs	Column and row maximums for HDF5Matrix
colMaxs.HDF5Matrix	Column and row maximums for HDF5Matrix
colMeans	Column and row means for HDF5Matrix
colMeans.HDF5Matrix	Column and row means for HDF5Matrix
colMins	Column and row minimums for HDF5Matrix
colMins.HDF5Matrix	Column and row minimums for HDF5Matrix
colnames.HDF5Matrix	Get dimension names of an HDF5Matrix
colnames<-.HDF5Matrix	Get dimension names of an HDF5Matrix
colSds	Column and row standard deviations for HDF5Matrix
colSds.HDF5Matrix	Column and row standard deviations for HDF5Matrix
colSums	Column and row sums for HDF5Matrix
colSums.HDF5Matrix	Column and row sums for HDF5Matrix
colVars	Column and row variances for HDF5Matrix
colVars.HDF5Matrix	Column and row variances for HDF5Matrix
cor	Correlation (generic)
cor.HDF5Matrix	Correlation matrix for HDF5Matrix objects
crossprod	Cross product of HDF5Matrix objects
crossprod.HDF5Matrix	Cross product of HDF5Matrix objects

-- D --

diag	Extract or construct a diagonal for HDF5Matrix
diag.default	Extract or construct a diagonal for HDF5Matrix
diag.HDF5Matrix	Extract or construct a diagonal for HDF5Matrix
diag<-	Set diagonal of an HDF5Matrix (generic)
diag_op	Diagonal-vector operation on an HDF5Matrix
diag_op.HDF5Matrix	Diagonal-vector operation on an HDF5Matrix
diag_scale	Scalar diagonal operation on an HDF5Matrix
diag_scale.HDF5Matrix	Scalar diagonal operation on an HDF5Matrix
dim.HDF5Matrix	Dimensions of an HDF5Matrix
dimnames.HDF5Matrix	Get dimension names of an HDF5Matrix
dimnames<-.HDF5Matrix	Set dimension names on an HDF5Matrix

-- E --

eigen	Spectral decomposition
eigen.default	Spectral decomposition
eigen.HDF5Matrix	Spectral decomposition

-- F --

filter_low_coverage	Remove high-missingness features from an HDF5Matrix
filter_low_coverage.HDF5Matrix	Remove high-missingness features from an HDF5Matrix
filter_maf	Remove SNPs by Minor Allele Frequency from an HDF5Matrix
filter_maf.HDF5Matrix	Remove SNPs by Minor Allele Frequency from an HDF5Matrix

-- G --

get_available_ram	Get available (free) system RAM
get_cpu_cores	Get number of CPU cores
get_memory_thresholds	Get dynamic memory thresholds based on system RAM
get_recommended_threads	Get recommended number of threads for parallel operations
get_total_ram	Get total system RAM

-- H --

HDF5Matrix-S3	S3 methods for HDF5Matrix
HDF5Matrix-scalar-aggregations	Summary statistics for HDF5Matrix
hdf5matrix_options	Set or get HDF5Matrix computation options
hdf5_apply	Apply a mathematical operation to multiple HDF5 datasets
hdf5_close_all	Close all HDF5Matrix objects
hdf5_close_file	Close all HDF5 handles for a specific file
hdf5_create_matrix	Create an HDF5 dataset and return an HDF5Matrix object
hdf5_import	Import data from file or URL into HDF5 format
hdf5_import_multiple	Import multiple files into HDF5
hdf5_matrix	Open an HDF5 dataset as an HDF5Matrix object
hdf5_reduce	Reduce all datasets in an HDF5 group by a binary operation

-- I --

impute_snps	Impute missing SNP values in an HDF5Matrix
impute_snps.HDF5Matrix	Impute missing SNP values in an HDF5Matrix
is_open	Check if HDF5Matrix is open

-- L --

length.HDF5Matrix	Length of an HDF5Matrix
list_datasets	List datasets in an HDF5 file or group

-- M --

mean.HDF5Matrix	Summary statistics for HDF5Matrix
memory_info	Print system memory information
miRNA	miRNA
multiply_sparse	Sparse-aware matrix multiplication (generic)
multiply_sparse.HDF5Matrix	Sparse-aware matrix multiplication for HDF5Matrix

-- O --

object_size	Get memory size of HDF5Matrix without loading
Ops.HDF5Matrix	Elementwise arithmetic operators for HDF5Matrix objects

-- P --

prcomp.HDF5Matrix	Principal Component Analysis of an HDF5Matrix
print.HDF5Matrix	Print an HDF5Matrix object
print.HDF5PCA	Print method for HDF5PCA objects
pseudoinverse	Moore-Penrose pseudoinverse
pseudoinverse.default	Moore-Penrose pseudoinverse
pseudoinverse.HDF5Matrix	Moore-Penrose pseudoinverse

-- Q --

qr	QR decomposition of an HDF5Matrix
qr.HDF5Matrix	QR decomposition of an HDF5Matrix

-- R --

rbind.HDF5Matrix	Row-bind HDF5Matrix objects
reduce	Reduce a group of HDF5 datasets by accumulation (generic)
rowMaxs	Column and row maximums for HDF5Matrix
rowMaxs.HDF5Matrix	Column and row maximums for HDF5Matrix
rowMeans	Column and row means for HDF5Matrix
rowMeans.HDF5Matrix	Column and row means for HDF5Matrix
rowMins	Column and row minimums for HDF5Matrix
rowMins.HDF5Matrix	Column and row minimums for HDF5Matrix
rownames.HDF5Matrix	Get dimension names of an HDF5Matrix
rownames<-.HDF5Matrix	Get dimension names of an HDF5Matrix
rowSds	Column and row standard deviations for HDF5Matrix
rowSds.HDF5Matrix	Column and row standard deviations for HDF5Matrix
rowSums	Column and row sums for HDF5Matrix
rowSums.HDF5Matrix	Column and row sums for HDF5Matrix
rowVars	Column and row variances for HDF5Matrix
rowVars.HDF5Matrix	Column and row variances for HDF5Matrix

-- S --

scale	Scale / normalize an HDF5Matrix
scale.HDF5Matrix	Scale / normalize an HDF5Matrix
sd	Standard deviation of all elements of an HDF5Matrix
sd.HDF5Matrix	Standard deviation of all elements of an HDF5Matrix
show_hdf5matrix_options	Show current HDF5Matrix performance settings
solve.HDF5Matrix	Matrix inverse of a symmetric positive-definite HDF5Matrix via Cholesky
split.HDF5Matrix	Split an HDF5Matrix into a list of blocks
split_dataset	Split an HDF5Matrix into multiple block datasets
split_dataset.HDF5Matrix	Split an HDF5Matrix into multiple block datasets
str.HDF5Matrix	Structure of an HDF5Matrix object
Summary.HDF5Matrix	Summary statistics for HDF5Matrix
svd	Singular Value Decomposition (generic)
svd.HDF5Matrix	Singular Value Decomposition of an HDF5Matrix
sweep	Sweep out array summaries (generic)
sweep.HDF5Matrix	Broadcast a vector over an HDF5Matrix (sweep)
system_info	Get system information summary

-- T --

tcrossprod	Transposed cross product of HDF5Matrix objects
tcrossprod.HDF5Matrix	Transposed cross product of HDF5Matrix objects

-- V --

var	Variance of all elements of an HDF5Matrix
var.HDF5Matrix	Variance of all elements of an HDF5Matrix

-- misc --

%*%	Matrix multiplication for HDF5Matrix
[.HDF5Matrix	Subset an HDF5Matrix
[<-.HDF5Matrix	Subsetting assignment for HDF5Matrix objects