Man pages for BigDataStatMeth
Title: Scalable Statistical Computing with HDF5-Backed Matrices
| apply_function | Apply a statistical or algebraic function to HDF5 datasets... |
| as.data.frame.HDF5Matrix | Convert HDF5Matrix to data.frame |
| as.matrix.HDF5Matrix | Convert HDF5Matrix to in-memory matrix |
| 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... |
| 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 |
| bd_wproduct | Weighted matrix–vector products and cross-products |
| bdWrite_hdf5_dimnames | Write dimnames to an HDF5 dataset |
| BigDataStatMeth | BigDataStatMeth: Scalable statistical computing with R, C++,... |
| can_allocate | Check if memory allocation is safe |
| cancer | Cancer classification |
| cbind.HDF5Matrix | Column-bind HDF5Matrix objects |
| chol.HDF5Matrix | Cholesky decomposition of a symmetric positive-definite... |
| close.HDF5Matrix | Close HDF5Matrix |
| colesterol | Dataset colesterol |
| colMaxs | Column and row maximums for HDF5Matrix |
| colMeans | Column and row means for HDF5Matrix |
| colMins | Column and row minimums for HDF5Matrix |
| colSds | Column and row standard deviations for HDF5Matrix |
| colSums | Column and row sums for HDF5Matrix |
| colVars | Column and row variances for HDF5Matrix |
| cor | Correlation (generic) |
| cor.HDF5Matrix | Correlation matrix for HDF5Matrix objects |
| crossprod.HDF5Matrix | Cross product of HDF5Matrix objects |
| diag | Extract or construct a diagonal for HDF5Matrix |
| diag_op | Diagonal-vector operation on an HDF5Matrix |
| diag-replace | Set diagonal of an HDF5Matrix (generic) |
| diag_scale | Scalar diagonal operation on an HDF5Matrix |
| dim.HDF5Matrix | Dimensions of an HDF5Matrix |
| dimnames.HDF5Matrix | Get dimension names of an HDF5Matrix |
| dimnames-set-.HDF5Matrix | Set dimension names on an HDF5Matrix |
| dot-get_option | Get global option value with fallback |
| dot-hdf5matrix_options | HDF5Matrix Global Options |
| dot-onUnload | Package hook: cleanup on unload |
| eigen | Spectral decomposition |
| filter_low_coverage | Remove high-missingness features from an HDF5Matrix |
| filter_maf | Remove SNPs by Minor Allele Frequency from an HDF5Matrix |
| 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 |
| 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 |
| hdf5matrix_options | Set or get HDF5Matrix computation options |
| HDF5Matrix-S3 | S3 methods for HDF5Matrix |
| HDF5Matrix-scalar-aggregations | Summary statistics for HDF5Matrix |
| hdf5_reduce | Reduce all datasets in an HDF5 group by a binary operation |
| impute_snps | Impute missing SNP values in an HDF5Matrix |
| is_open | Check if HDF5Matrix is open |
| length.HDF5Matrix | Length of an HDF5Matrix |
| list_datasets | List datasets in an HDF5 file or group |
| matmul | Matrix multiplication 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 |
| object_size | Get memory size of HDF5Matrix without loading |
| Ops.HDF5Matrix | Elementwise arithmetic operators for HDF5Matrix objects |
| 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 |
| qr | QR decomposition of an HDF5Matrix |
| qr.HDF5Matrix | QR decomposition of an HDF5Matrix |
| rbind.HDF5Matrix | Row-bind HDF5Matrix objects |
| rcpp_hdf5_close_all_file_handles | Close all open HDF5 file handles mid-session (safe) |
| rcpp_hdf5_close_all_registry | Close all open HDF5Dataset objects and HDF5 handles |
| rcpp_hdf5_close_at_paths | Close all live HDF5Matrix handles pointing to specific... |
| rcpp_hdf5_close_file_handles | Close all HDF5 handles for a specific file (R6 wrapper) |
| rcpp_hdf5_close_file_handles_safe | Safely close all remaining HDF5 file handles (mid-session... |
| rcpp_hdf5_create_matrix | Create an HDF5 dataset with configurable compression (R6... |
| rcpp_hdf5dataset_add | Element-wise addition of two HDF5 datasets (R6 wrapper) |
| rcpp_hdf5dataset_close | Close and destroy an HDF5 dataset handle immediately. |
| rcpp_hdf5dataset_colMaxs | Column maximums of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_colMeans | Column means of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_colMins | Column minimums of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_colSds | Column standard deviations of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_colSums | Column sums of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_colVars | Column variances of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_crossprod | Cross product for HDF5 datasets (R6 wrapper) |
| rcpp_hdf5dataset_dim | Get dimensions of HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_div_ew | Element-wise division of two HDF5 datasets (R6 wrapper) |
| rcpp_hdf5dataset_info | Get dataset information (R6 wrapper) |
| rcpp_hdf5dataset_is_valid | Check if dataset is valid and open (R6 wrapper) |
| rcpp_hdf5dataset_mul_ew | Element-wise multiplication of two HDF5 datasets (R6 wrapper) |
| rcpp_hdf5dataset_multiply | General matrix product for HDF5 datasets (R6 wrapper) |
| rcpp_hdf5dataset_open | Open HDF5 dataset and return external pointer (R6 wrapper) |
| rcpp_hdf5dataset_read_all | Get full dataset as matrix (convenience function) |
| rcpp_hdf5dataset_read_dimnames | Read dimension names (rownames / colnames) from an HDF5... |
| rcpp_hdf5dataset_rowMaxs | Row maximums of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_rowMeans | Row means of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_rowMins | Row minimums of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_rowSds | Row standard deviations of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_rowSums | Row sums of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_rowVars | Row variances of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_scalar_max | Maximum of all elements of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_scalar_mean | Mean of all elements of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_scalar_min | Minimum of all elements of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_scalar_sd | Standard deviation of all elements of an HDF5 dataset (R6... |
| rcpp_hdf5dataset_scalar_sum | Sum of all elements of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_scalar_var | Variance of all elements of an HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_subset | Read block from HDF5 dataset (subsetting) |
| rcpp_hdf5dataset_subtract | Element-wise subtraction of two HDF5 datasets (R6 wrapper) |
| rcpp_hdf5dataset_tcrossprod | Transposed cross product for HDF5 datasets (R6 wrapper) |
| rcpp_hdf5dataset_write_all | Write entire dataset (R6 wrapper) |
| rcpp_hdf5dataset_write_block | Write data block to HDF5 dataset (R6 wrapper) |
| rcpp_hdf5dataset_write_dimnames | Write dimension names through the R6 dataset handle |
| reduce | Reduce a group of HDF5 datasets by accumulation (generic) |
| scale | Scale / normalize 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... |
| split_dataset | Split an HDF5Matrix into multiple block datasets |
| split.HDF5Matrix | Split an HDF5Matrix into a list of blocks |
| str.HDF5Matrix | Structure of an HDF5Matrix object |
| sub-.HDF5Matrix | Subset an HDF5Matrix |
| subset-.HDF5Matrix | Subsetting assignment for HDF5Matrix objects |
| 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 |
| tcrossprod.HDF5Matrix | Transposed cross product of HDF5Matrix objects |
| var.HDF5Matrix | Variance of all elements of an HDF5Matrix |
