# Scalable Statistical Computing with HDF5-Backed Matrices

## Documentation for package ‘BigDataStatMeth’ version 2.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
pseudoinverse.matrix | 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