diff --git a/.Rbuildignore b/.Rbuildignore index 8228aa5..0098e3c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -5,8 +5,4 @@ ^pkgdown$ ^\.github$ ^INSTALLATION\.md$ -^environment\.yml$ -^CONTRIBUTING\.md$ -^CODE_OF_CONDUCT\.md$ ^dev$ -^cran-comments\.md$ diff --git a/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md similarity index 100% rename from CODE_OF_CONDUCT.md rename to .github/CODE_OF_CONDUCT.md diff --git a/CONTRIBUTING.md b/.github/CONTRIBUTING.md similarity index 100% rename from CONTRIBUTING.md rename to .github/CONTRIBUTING.md diff --git a/.gitignore b/.gitignore index 45e06f5..54a922f 100644 --- a/.gitignore +++ b/.gitignore @@ -7,6 +7,9 @@ .ipynb_checkpoints inst/doc docs/ +*.tar.gz +src/*.so +src/*.o .* !/.gitignore !/.github \ No newline at end of file diff --git a/INSTALLATION.md b/INSTALLATION.md index 43e88e9..1c99866 100644 --- a/INSTALLATION.md +++ b/INSTALLATION.md @@ -1,48 +1,133 @@ -## Installation +# Installation -- You can install the development version of SelectSim from - [GitHub](https://github.com/CSOgroup/SelectSim) with: +## Prerequisites -``` r +SelectSim requires **R ≥ 3.5** and includes compiled C++ code via `Rcpp` and `RcppArmadillo`. +Before installing, make sure you have a working C++ compiler: + +- **macOS** — Install Xcode Command Line Tools: `xcode-select --install` +- **Linux** — Install build tools, e.g. on Ubuntu/Debian: `sudo apt install build-essential` +- **Windows** — Install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) and ensure it is on your PATH + +--- + +## Option 1 — Install from GitHub (standard) + +Install directly from GitHub using `pak`: + +```r +# install.packages("pak") +pak::pak("CSOgroup/SelectSim") +``` + +Or using `devtools` (legacy): + +```r # install.packages("devtools") -devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE) +devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE) ``` -## Installation with micromamba enviorment (prefered) +--- +## Option 2 — Install with micromamba (recommended) -`micromamba` is a tiny version of the mamba package manager (Like Conda). Refer [website](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) for it's installation guide. +[micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) provides a fully isolated, reproducible R environment. This is the **recommended approach** if you are on a shared server, HPC cluster, or want to avoid conflicts with your existing R installation. -Steps to follow after installing micromamba in a terminal: +### Step 1 — Install micromamba -`micromamba create -n r_env`\ -`micromamba activate r_env`\ -`micromamba install conda-forge::r-base`\ -`micromamba install conda-forge::r-essentials`\ -`micromamba install conda-forge::r-devtools`\ -`micromamba install conda-forge::r-pak`\ -`micromamba install conda-forge::cmake`\ -`micromamba install conda-forge::r-rcppparallel`\ -`micromamba install conda-forge::r-rfast` +Follow the [official micromamba installation guide](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) for your platform. -- After this run R and install `SelectSim` R package as follows -``` r -# install.packages("devtools") -devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE) +### Step 2 — Create and activate an R environment + +```bash +micromamba create -n r_env +micromamba activate r_env ``` -OR -``` r -library('pak') -pak::pkg_install('CSOgroup/SelectSim') + +### Step 3 — Install R and required system dependencies + +```bash +micromamba install \ + conda-forge::r-base \ + conda-forge::r-essentials \ + conda-forge::r-devtools \ + conda-forge::r-pak \ + conda-forge::cmake \ + conda-forge::r-rcppparallel \ + conda-forge::r-rfast ``` -Alternative way install with provided [`enviorment.yml`](enviorment.yml) file. +### Step 4 — Install SelectSim inside R -`micromamba create -f enviorment.yml`\ -`micromamba activate r_env` -- After this run R and install `SelectSim` R package as follows -``` r -# install.packages("devtools") -devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE) +```r +# install.packages("pak") +pak::pak("CSOgroup/SelectSim") +``` + +--- + +## Option 3 — Restore the exact development environment + +A fully pinned conda environment file is provided at [`dev/environment.yml`](dev/environment.yml). +This reproduces the exact software stack (R version, all system libraries) used during development. + +```bash +micromamba create -f dev/environment.yml +micromamba activate r_env ``` +Then install SelectSim: + +```r +pak::pak("CSOgroup/SelectSim") +``` + +> **Note:** The environment file pins exact package versions and is Linux-specific (linux-64). +> It may not work on macOS or Windows. + +--- + +## Verifying the installation + +After installing, confirm everything works with a quick test run: + +```r +library(SelectSim) +data(luad_run_data, package = "SelectSim") + +result <- selectX( + M = luad_run_data$M, + sample.class = luad_run_data$sample.class, + alteration.class = luad_run_data$alteration.class, + n.cores = 1, + min.freq = 10, + n.permut = 10 # small number for a quick smoke test +) +``` + +A successful run returns a list with a `result` data frame of evolutionary dependencies. +For a full analysis, use `n.permut = 1000` or higher. + +--- + +## Troubleshooting + +**`rfast` fails to install** +`rfast` requires a Fortran compiler. +On macOS, install `gfortran` from [mac.r-project.org/tools](https://mac.r-project.org/tools/). +On Linux, install via your package manager (e.g. `sudo apt install gfortran`). +With micromamba, `conda-forge::r-rfast` handles this automatically. + +**Vignettes not building** +Ensure `pandoc` is installed (`pandoc --version` in a terminal). +Install via `brew install pandoc` (macOS), `sudo apt install pandoc` (Linux), or through the micromamba environment (`conda-forge::pandoc`). + +**Compilation errors on Windows** +Ensure Rtools is installed and its `bin/` directory is on your PATH. +Run `pkgbuild::check_build_tools()` in R to verify your toolchain is detected correctly. + +**Vignettes missing after install** +`pak::pak()` does not build vignettes by default. If you need the vignettes locally, use: +```r +devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE) +``` diff --git a/README.Rmd b/README.Rmd index 3b914c9..fedeaed 100644 --- a/README.Rmd +++ b/README.Rmd @@ -35,8 +35,8 @@ This package accompanies the manuscript: You can install the development version of SelectSim from [GitHub](https://github.com/CSOgroup/SelectSim) with: ``` r -# install.packages("devtools") -devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE) +# install.packages("pak") +pak::pak("CSOgroup/SelectSim") ``` For more details on installation refer to [INSTALLATION](INSTALLATION.md). diff --git a/README.md b/README.md index 9d88d33..19947c2 100644 --- a/README.md +++ b/README.md @@ -38,8 +38,8 @@ You can install the development version of SelectSim from [GitHub](https://github.com/CSOgroup/SelectSim) with: ``` r -# install.packages("devtools") -devtools::install_github("CSOgroup/SelectSim", dependencies = TRUE, build_vignettes = TRUE) +# install.packages("pak") +pak::pak("CSOgroup/SelectSim") ``` For more details on installation refer to diff --git a/cran-comments.md b/dev/cran-comments.md similarity index 100% rename from cran-comments.md rename to dev/cran-comments.md diff --git a/environment.yml b/dev/environment.yml similarity index 100% rename from environment.yml rename to dev/environment.yml diff --git a/man/GENIE_maf_schema.Rd b/man/GENIE_maf_schema.Rd index 109a048..ddda289 100644 --- a/man/GENIE_maf_schema.Rd +++ b/man/GENIE_maf_schema.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{GENIE_maf_schema} \alias{GENIE_maf_schema} \title{GENIE_maf_schema: schema for GENIE maf file to process the mutations} diff --git a/man/TCGA_maf_schema.Rd b/man/TCGA_maf_schema.Rd index ec59f97..cdc932a 100644 --- a/man/TCGA_maf_schema.Rd +++ b/man/TCGA_maf_schema.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{TCGA_maf_schema} \alias{TCGA_maf_schema} \title{TCGA_maf_schema: schema for TCGA maf file to process the mutations} diff --git a/man/add.Rd b/man/add.Rd index 60d2ab6..9317ed9 100644 --- a/man/add.Rd +++ b/man/add.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{add} \alias{add} \title{Sum a list of matrices element-wise} diff --git a/man/al.pairwise.alteration.stats.Rd b/man/al.pairwise.alteration.stats.Rd index 23952c0..c3fd554 100644 --- a/man/al.pairwise.alteration.stats.Rd +++ b/man/al.pairwise.alteration.stats.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{al.pairwise.alteration.stats} \alias{al.pairwise.alteration.stats} \title{Compute pairwise alteration statistics for an alteration landscape} diff --git a/man/al.stats.Rd b/man/al.stats.Rd index 6a35d44..96c8cf3 100644 --- a/man/al.stats.Rd +++ b/man/al.stats.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{al.stats} \alias{al.stats} \title{Compute alteration landscape statistics} diff --git a/man/am.pairwise.alteration.coverage.Rd b/man/am.pairwise.alteration.coverage.Rd index 85429f2..93223c7 100644 --- a/man/am.pairwise.alteration.coverage.Rd +++ b/man/am.pairwise.alteration.coverage.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{am.pairwise.alteration.coverage} \alias{am.pairwise.alteration.coverage} \title{Compute pairwise alteration coverage statistics} diff --git a/man/am.pairwise.alteration.overlap.Rd b/man/am.pairwise.alteration.overlap.Rd index 7655c6a..0e76342 100644 --- a/man/am.pairwise.alteration.overlap.Rd +++ b/man/am.pairwise.alteration.overlap.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{am.pairwise.alteration.overlap} \alias{am.pairwise.alteration.overlap} \title{Compute pairwise alteration co-occurrence counts} diff --git a/man/am.stats.Rd b/man/am.stats.Rd index 87b9bd4..e48218c 100644 --- a/man/am.stats.Rd +++ b/man/am.stats.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{am.stats} \alias{am.stats} \title{Compute summary statistics for a binary alteration matrix} diff --git a/man/am.weight.pairwise.alteration.overlap.Rd b/man/am.weight.pairwise.alteration.overlap.Rd index 20a0c55..65f2af7 100644 --- a/man/am.weight.pairwise.alteration.overlap.Rd +++ b/man/am.weight.pairwise.alteration.overlap.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{am.weight.pairwise.alteration.overlap} \alias{am.weight.pairwise.alteration.overlap} \title{Compute TMB-weighted pairwise alteration overlap} diff --git a/man/binary.yule.Rd b/man/binary.yule.Rd index 8574361..4dfcf9d 100644 --- a/man/binary.yule.Rd +++ b/man/binary.yule.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{binary.yule} \alias{binary.yule} \title{Compute Yule Q coefficient for all gene pairs} diff --git a/man/effectSize.Rd b/man/effectSize.Rd index 484cf01..a47c683 100644 --- a/man/effectSize.Rd +++ b/man/effectSize.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{effectSize} \alias{effectSize} \title{Compute effect size between observed and expected overlap} diff --git a/man/estimateFDR2.Rd b/man/estimateFDR2.Rd index 9b2ea6b..d4348f4 100644 --- a/man/estimateFDR2.Rd +++ b/man/estimateFDR2.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{estimateFDR2} \alias{estimateFDR2} \title{Estimate FDR by scanning observed vs null effect sizes} diff --git a/man/estimate_p_val.Rd b/man/estimate_p_val.Rd index 2c3410f..a79b9b4 100644 --- a/man/estimate_p_val.Rd +++ b/man/estimate_p_val.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{estimate_p_val} \alias{estimate_p_val} \title{Compute empirical two-sided p-value for a gene pair} diff --git a/man/estimate_pairwise_p.Rd b/man/estimate_pairwise_p.Rd index 6a0858e..2c87033 100644 --- a/man/estimate_pairwise_p.Rd +++ b/man/estimate_pairwise_p.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{estimate_pairwise_p} \alias{estimate_pairwise_p} \title{Compute p-values for all gene pairs in a results table} diff --git a/man/filter_maf_column.Rd b/man/filter_maf_column.Rd index 6a38ff9..89b7843 100644 --- a/man/filter_maf_column.Rd +++ b/man/filter_maf_column.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_column} \alias{filter_maf_column} \title{Filter maf function} diff --git a/man/filter_maf_complex.Rd b/man/filter_maf_complex.Rd index 6f20b2d..126a09f 100644 --- a/man/filter_maf_complex.Rd +++ b/man/filter_maf_complex.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_complex} \alias{filter_maf_complex} \title{Filter a MAF dataframe by a combination of column values} diff --git a/man/filter_maf_gene.name.Rd b/man/filter_maf_gene.name.Rd index 14c64fd..a39e7e4 100644 --- a/man/filter_maf_gene.name.Rd +++ b/man/filter_maf_gene.name.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_gene.name} \alias{filter_maf_gene.name} \title{Filter a MAF dataframe by gene name} diff --git a/man/filter_maf_ignore.Rd b/man/filter_maf_ignore.Rd index b5da61d..40d4a30 100644 --- a/man/filter_maf_ignore.Rd +++ b/man/filter_maf_ignore.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_ignore} \alias{filter_maf_ignore} \title{This function filters a MAF dataframe by retaining (or discarding) ignore mutations} diff --git a/man/filter_maf_missense.Rd b/man/filter_maf_missense.Rd index 894aeeb..16c844b 100644 --- a/man/filter_maf_missense.Rd +++ b/man/filter_maf_missense.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_missense} \alias{filter_maf_missense} \title{This function filters a MAF dataframe by retaining (or discarding) missense mutations} diff --git a/man/filter_maf_mutation.type.Rd b/man/filter_maf_mutation.type.Rd index b56c93e..917e0d2 100644 --- a/man/filter_maf_mutation.type.Rd +++ b/man/filter_maf_mutation.type.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_mutation.type} \alias{filter_maf_mutation.type} \title{Filter a MAF dataframe by mutation type} diff --git a/man/filter_maf_mutations.Rd b/man/filter_maf_mutations.Rd index db7d824..847f62e 100644 --- a/man/filter_maf_mutations.Rd +++ b/man/filter_maf_mutations.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_mutations} \alias{filter_maf_mutations} \title{Filter a MAF dataframe by specific gene-mutation combinations} diff --git a/man/filter_maf_sample.Rd b/man/filter_maf_sample.Rd index 7487932..6d0bc9b 100644 --- a/man/filter_maf_sample.Rd +++ b/man/filter_maf_sample.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_sample} \alias{filter_maf_sample} \title{Filter a MAF dataframe by sample ID} diff --git a/man/filter_maf_schema.Rd b/man/filter_maf_schema.Rd index a8b8107..0153018 100644 --- a/man/filter_maf_schema.Rd +++ b/man/filter_maf_schema.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_schema} \alias{filter_maf_schema} \title{This function filters a MAF dataframe by sample id} diff --git a/man/filter_maf_truncating.Rd b/man/filter_maf_truncating.Rd index 70e6a06..a99f2d3 100644 --- a/man/filter_maf_truncating.Rd +++ b/man/filter_maf_truncating.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{filter_maf_truncating} \alias{filter_maf_truncating} \title{This function filters a MAF dataframe by retaining (or discarding) truncating mutations} diff --git a/man/generateS.Rd b/man/generateS.Rd index d4ea962..478a6a1 100644 --- a/man/generateS.Rd +++ b/man/generateS.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{generateS} \alias{generateS} \title{Generate S matrix} diff --git a/man/generateW_block.Rd b/man/generateW_block.Rd index 551a611..74afead 100644 --- a/man/generateW_block.Rd +++ b/man/generateW_block.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{generateW_block} \alias{generateW_block} \title{Generate block-aware sample weight matrix} diff --git a/man/generateW_mean_tmb.Rd b/man/generateW_mean_tmb.Rd index bb6efa7..2c7aa7b 100644 --- a/man/generateW_mean_tmb.Rd +++ b/man/generateW_mean_tmb.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{generateW_mean_tmb} \alias{generateW_mean_tmb} \title{Generate sample weight matrix from TMB values} diff --git a/man/get.blocks.Rd b/man/get.blocks.Rd index c3a06a0..6d5633d 100644 --- a/man/get.blocks.Rd +++ b/man/get.blocks.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{get.blocks} \alias{get.blocks} \title{Get sample/alteration blocks} diff --git a/man/interaction.table.Rd b/man/interaction.table.Rd index ad90dee..825e58a 100644 --- a/man/interaction.table.Rd +++ b/man/interaction.table.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{interaction.table} \alias{interaction.table} \title{Build the full interaction results table from selectX outputs} diff --git a/man/maf2gam.Rd b/man/maf2gam.Rd index 711acc7..4db96ec 100644 --- a/man/maf2gam.Rd +++ b/man/maf2gam.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{maf2gam} \alias{maf2gam} \title{Generate gam from the maf file} diff --git a/man/mutation_type.Rd b/man/mutation_type.Rd index b26cb8a..e173ca1 100644 --- a/man/mutation_type.Rd +++ b/man/mutation_type.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{mutation_type} \alias{mutation_type} \title{Mutation list object} diff --git a/man/new.AL.general.Rd b/man/new.AL.general.Rd index 6bf81df..aa349ad 100644 --- a/man/new.AL.general.Rd +++ b/man/new.AL.general.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{new.AL.general} \alias{new.AL.general} \title{Create an Alteration Landscape (AL) object} diff --git a/man/new.ALS.Rd b/man/new.ALS.Rd index 438af41..8e74791 100644 --- a/man/new.ALS.Rd +++ b/man/new.ALS.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{new.ALS} \alias{new.ALS} \title{Initialize an Alteration Landscape Stats (ALS) container} diff --git a/man/new.AMS.Rd b/man/new.AMS.Rd index d74c2e7..c209bb8 100644 --- a/man/new.AMS.Rd +++ b/man/new.AMS.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{new.AMS} \alias{new.AMS} \title{Initialize an Alteration Matrix Stats (AMS) container} diff --git a/man/null_model_parallel.Rd b/man/null_model_parallel.Rd index 182c17c..29f275f 100644 --- a/man/null_model_parallel.Rd +++ b/man/null_model_parallel.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{null_model_parallel} \alias{null_model_parallel} \title{Generating the null_simulation matrix} diff --git a/man/r.am.pairwise.alteration.overlap.Rd b/man/r.am.pairwise.alteration.overlap.Rd index cec23ff..9634376 100644 --- a/man/r.am.pairwise.alteration.overlap.Rd +++ b/man/r.am.pairwise.alteration.overlap.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{r.am.pairwise.alteration.overlap} \alias{r.am.pairwise.alteration.overlap} \title{Compute null overlap matrix} diff --git a/man/r.effectSize.Rd b/man/r.effectSize.Rd index 26bcbb8..5c2d0d8 100644 --- a/man/r.effectSize.Rd +++ b/man/r.effectSize.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{r.effectSize} \alias{r.effectSize} \title{Compute effect sizes for null model permutations} diff --git a/man/retrieveOutliers.Rd b/man/retrieveOutliers.Rd index 6e4a9a7..af826a6 100644 --- a/man/retrieveOutliers.Rd +++ b/man/retrieveOutliers.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{retrieveOutliers} \alias{retrieveOutliers} \title{Identify outlier null-model matrices} diff --git a/man/stat_maf_column.Rd b/man/stat_maf_column.Rd index b3a8a11..1307c5b 100644 --- a/man/stat_maf_column.Rd +++ b/man/stat_maf_column.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{stat_maf_column} \alias{stat_maf_column} \title{Summary functions for MAF file} diff --git a/man/stat_maf_gene.Rd b/man/stat_maf_gene.Rd index a646973..26d4873 100644 --- a/man/stat_maf_gene.Rd +++ b/man/stat_maf_gene.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{stat_maf_gene} \alias{stat_maf_gene} \title{Count mutations per gene in a MAF file} diff --git a/man/stat_maf_sample.Rd b/man/stat_maf_sample.Rd index 03be6ef..34bbc77 100644 --- a/man/stat_maf_sample.Rd +++ b/man/stat_maf_sample.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/gam_utils.R +% Please edit documentation in R/gam_utils.r \name{stat_maf_sample} \alias{stat_maf_sample} \title{Count mutations per sample in a MAF file} diff --git a/man/template.obj.gen.Rd b/man/template.obj.gen.Rd index 96bfb7e..9800f54 100644 --- a/man/template.obj.gen.Rd +++ b/man/template.obj.gen.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_create.R +% Please edit documentation in R/selectX_create.r \name{template.obj.gen} \alias{template.obj.gen} \title{Generate the template matrix} diff --git a/man/w.r.am.pairwise.alteration.overlap.Rd b/man/w.r.am.pairwise.alteration.overlap.Rd index 4ed193d..fd6d71d 100644 --- a/man/w.r.am.pairwise.alteration.overlap.Rd +++ b/man/w.r.am.pairwise.alteration.overlap.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/selectX_stats.R +% Please edit documentation in R/selectX_stats.r \name{w.r.am.pairwise.alteration.overlap} \alias{w.r.am.pairwise.alteration.overlap} \title{Compute null weighted overlap matrix} diff --git a/src/SelectSim.so b/src/SelectSim.so deleted file mode 100755 index 2736c7d..0000000 Binary files a/src/SelectSim.so and /dev/null differ