diff --git a/DESCRIPTION b/DESCRIPTION index 1701095..808d679 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: splikit -Title: A Toolkit for Analysing RNA Splicing in scRNA-Seq Data +Title: A Toolkit for Analysing RNA Splicing in Single-cell RNA Sequencing Data Version: 2.0.0 Authors@R: person("Arsham", "Mikaeili Namini", , "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre"), diff --git a/README.md b/README.md index c132dd6..44f0887 100644 --- a/README.md +++ b/README.md @@ -8,8 +8,8 @@ ## **Requirements** -- [R version 3.5.0](http://www.r-project.org/) or later. -- R libraries: [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html), [RcppArmadillo](https://cran.r-project.org/web/packages/RcppArmadillo/index.html), [Matrix](https://cran.r-project.org/web/packages/Matrix/index.html), [data.table](https://cran.r-project.org/web/packages/data.table/index.html), [R6](https://cran.r-project.org/web/packages/R6/index.html) +- [R version 3.5.0](https://r-project.org/) or later. +- R libraries: [Rcpp](https://CRAN.R-project.org/package=Rcpp), [RcppArmadillo](https://CRAN.R-project.org/package=RcppArmadillo), [Matrix](https://CRAN.R-project.org/package=Matrix), [data.table](https://CRAN.R-project.org/package=data.table), [R6](https://CRAN.R-project.org/package=R6) ## Installation diff --git a/man/get_pseudo_correlation.Rd b/man/get_pseudo_correlation.Rd index bbd7b6d..227c9ac 100644 --- a/man/get_pseudo_correlation.Rd +++ b/man/get_pseudo_correlation.Rd @@ -49,6 +49,8 @@ m1_inclusion <- m1_obj$m1_inclusion_matrix eventdata <- m1_obj$event_data m2_exclusion <- make_m2(m1_inclusion, eventdata) +\donttest{ + # creating a dummy ZDB ZDB_matrix <- matrix(rnorm(n = (nrow(m1_inclusion) * ncol(m1_inclusion)), sd = 7), nrow = nrow(m1_inclusion), @@ -62,12 +64,5 @@ m2_dense <- as.matrix(m2_exclusion) pseudo_r_square_cox <- get_pseudo_correlation(ZDB_matrix, m1_dense, m2_dense) print(pseudo_r_square_cox) -# Example with sparse matrices (more memory efficient) -pseudo_r_square_sparse <- get_pseudo_correlation(ZDB_matrix, m1_inclusion, m2_exclusion) - -# Example using Nagelkerke R² instead of Cox-Snell -pseudo_r_square_nagel <- get_pseudo_correlation(ZDB_matrix, m1_inclusion, m2_exclusion, - metric = "Nagelkerke") -print(pseudo_r_square_nagel) - + } } diff --git a/src/Makevars b/src/Makevars index 6660c7f..3a7f8ac 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,3 +1,2 @@ -CXX_STD = CXX14 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) diff --git a/src/Makevars.win b/src/Makevars.win index 85d1c66..3a7f8ac 100644 --- a/src/Makevars.win +++ b/src/Makevars.win @@ -1,4 +1,2 @@ -## src/Makevars.win (Windows) -CXX_STD = CXX14 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)