Package: bigstatsr 1.6.1
Florian Privé
bigstatsr: Statistical Tools for Filebacked Big Matrices
Easy-to-use, efficient, flexible and scalable statistical tools. Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping. It provides for instance matrix operations, Principal Component Analysis, sparse linear supervised models, utility functions and more <doi:10.1093/bioinformatics/bty185>.
Authors:
bigstatsr_1.6.1.tar.gz
bigstatsr_1.6.1.tar.gz(r-4.5-noble)bigstatsr_1.6.1.tar.gz(r-4.4-noble)
bigstatsr_1.6.1.tgz(r-4.4-emscripten)bigstatsr_1.6.1.tgz(r-4.3-emscripten)
bigstatsr.pdf |bigstatsr.html✨
bigstatsr/json (API)
NEWS
| # Install 'bigstatsr' in R: |
| install.packages('bigstatsr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/privefl/bigstatsr/issues
Last updated 3 months agofrom:ad9b1584e4. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 09 2024 |
| R-4.5-linux-x86_64 | OK | Nov 09 2024 |
Exports:add_code256as_FBMas_scaling_funasPlotlyTextAUCAUCBootbig_applybig_attachbig_attachExtdatabig_colstatsbig_copybig_corbig_countsbig_cprodMatbig_cprodVecbig_crossprodSelfbig_incrementbig_parallelizebig_prodMatbig_prodVecbig_randomSVDbig_readbig_scalebig_spLinRegbig_spLogRegbig_SVDbig_tcrossprodSelfbig_transposebig_univLinRegbig_univLogRegbig_writeblock_sizecols_alongcovar_from_dfdiagFBMFBM.code256get_betanb_corespasteLocpcorplot_gridplusrows_alongsub_bktheme_bigstatsrtypeofwithout_downcast_warning
Dependencies:bigassertrbigparallelrbitclicodetoolscolorspacecowplotdoParallelfansifarverffflockforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigpsR6RColorBrewerRcppRcppArmadilloRcppEigenRhpcBLASctlrlangrmioRSpectrascalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Scaling function creator | as_scaling_fun |
| Plotly text | asPlotlyText |
| AUC | AUC AUCBoot |
| Split-Apply-Combine | big_apply |
| Standard univariate statistics | big_colstats |
| Copy as a Filebacked Big Matrix | big_copy |
| Correlation | big_cor |
| Counts for class FBM.code256 | big_counts |
| Cross-product with a matrix | big_cprodMat crossprod,FBM,matrix-method crossprod,matrix,FBM-method tcrossprod,FBM,matrix-method tcrossprod,matrix,FBM-method |
| Cross-product with a vector | big_cprodVec |
| Crossprod | big_crossprodSelf crossprod,FBM,missing-method |
| Increment an FBM | big_increment |
| Split-parApply-Combine | big_parallelize |
| Product with a matrix | %*%,FBM,matrix-method %*%,matrix,FBM-method big_prodMat |
| Product with a vector | big_prodVec |
| Randomized partial SVD | big_randomSVD |
| Read a file as FBM | big_read |
| Some scaling functions | big_scale |
| Sparse linear regression | big_spLinReg |
| Sparse logistic regression | big_spLogReg |
| Partial SVD | big_SVD |
| Tcrossprod | big_tcrossprodSelf tcrossprod,FBM,missing-method |
| Transpose an FBM | big_transpose |
| Column-wise linear regression | big_univLinReg |
| Column-wise logistic regression | big_univLogReg |
| Write an FBM to a file | big_write |
| Determine a correct value for the block.size parameter | block_size |
| Numeric matrix from data frame | covar_from_df |
| Class FBM | as_FBM FBM FBM-class FBM_RC |
| Methods for the FBM class | diag,FBM-method dim,FBM-method FBM-methods length,FBM-method typeof,FBM-method [,FBM,ANY,ANY,ANY-method [<-,FBM,ANY,ANY,ANY-method |
| Class FBM.code256 | add_code256 FBM.code256 FBM.code256-class FBM.code256_RC |
| Combine sets of coefficients | get_beta |
| Get coordinates on plot | pasteLoc |
| Partial correlation | pcor |
| Plot method | plot.big_sp_list |
| Plot method | plot.big_SVD |
| Plot method | plot.mhtest |
| Predict method | predict.big_sp |
| Predict method | predict.big_sp_list |
| Scores of PCA | predict.big_SVD |
| Predict method | predict.mhtest |
| Replace extension '.bk' | sub_bk |
| Summary method | summary.big_sp_list |
| Theme ggplot2 | theme_bigstatsr |
| Temporarily disable downcast warning | without_downcast_warning |
