Modify Main_mean_NB_spBay.
Activate "Allow sparse matrix as output (valid only for mean version procedure)". Hence you can work on dgCMatrix throughout the process. Input which is not of type dgCMatrix will be converted to dgCMatrix at first.
Deprecated: Allow sparse matrix as output (valid only for mean version procedure). Since sparse matrix is useful only when the matrix it is sparse.
Calibrate documentations.
Allow sparse matrix as output (valid only for mean version procedure).
Let version of RELEASE_3_10 to be 1.4.11.
Update RELEASE_3_10 1.4.2 to 1.4.3.
Change back to Rcpp EstPrior function (sp_mat version).
Use dgCMatrix instead of matrix in R.
define ARMA\_64BIT\_WORD 1 and so on allows for big sparse matrix (learn from the liger R package).
Change back to rowSums instead of using Rcpp EstPrior function.
Add useful function file.
Use Rcpp EstPrior function.
as_matrix for transforming sparse matrix to matrix in R efficiently than as.matrix.
Make BB_fun faster: speed up the access of row of dgCMatrix object.
Modify EstPrior, using rowSums from Matrix package to calculated variance. Hence no need for Rcpp EstPrior function.
Support sparse matrix: dgTMatrix and dgCMatrix.
Add Rcpp EstPrior function.
Vectorize computation in EstPrior function.
Set default setting of BETA_vec=NULL.
Update citation.
Suppress warning message came from BiocParallel.
For a smoother progress bar, use foreach instead of BiocParallel.
Replacing foreach with BiocParallel
Fix some errors in BB_fun
Let more examples to be runnable; Updated vignette; Including SingleCellExperiment Class.
Fix some errors.
Apply corrections proposed by the reviewer, for more details please see https://github.com/Bioconductor/Contributions/issues/878
Fix two warnings reported by Bioconductor
WARNING: Use TRUE/FALSE instead of T/F, Found in files: tests/testthat/test-bayNorm.r
WARNING: Use is() or !is()
Pass all checks of both R CMD build and R CMD BiocCheck.
Future work:
Vignette needs to be further improved.
Need to Improve man pages.
Submit to Bioconductor.