Prepare SelectSim 0.1.6 for CRAN submission

.Rbuildignore

@@ -6,3 +6,4 @@
 ^\.github$
 ^INSTALLATION\.md$
 ^dev$
+^cran-comments\.md$

DESCRIPTION

@@ -1,16 +1,20 @@
 Package: SelectSim
-Title: Selected Events Linked by Evolutionary Conditions Across Human Tumors
+Title: Selected Events Linked by Evolutionary Conditions in Cancer
 Version: 0.1.6
 Authors@R: c(
-    person("Arvind", "Iyer", , "ayalurarvind@gmail.com", role = c("aut", "cre"),
+    person("Arvind", "Iyer", , "ayalurarvind@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-8247-700X")),
     person("Marco", "Mina", , "marco.mina.85@gmail.com", role = "aut"),
-    person("Miljan", "Petrovic", , "miljanpet93@gmail.com", role = "aut"),
-    person("Giovanni", "Ciriello", , "giovanni.ciriello@unil.ch", role = "aut",
+    person("Miljan", "Petrovic", , "miljanpet93@gmail.com", role = c("aut", "cph")),
+    person("Giovanni", "Ciriello", , "giovanni.ciriello@unil.ch", role = c("aut", "cph"),
            comment = c(ORCID = "0000-0003-2021-8683"))
   )
-Description: This R package implements the SelectSim methodology to infer
-    co-mutations between functional alterations in cancer.
+Description: Implements the 'SelectSim' methodology for identifying patterns of
+    co-occurrence and mutual exclusivity between functional genomic alterations
+    in cancer cohorts. The package processes mutation annotation data, constructs
+    alteration matrices, estimates expected alteration-pair frequencies, and
+    quantifies deviations associated with selective interactions. The methodology
+    is described in Iyer et al. (2026) <doi:10.1038/s41588-026-02661-4>.
 License: MIT + file LICENSE
 URL: https://csogroup.github.io/SelectSim/
 BugReports: https://github.com/CSOgroup/SelectSim/issues

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2025
+YEAR: 2026
 COPYRIGHT HOLDER: SelectSim authors

NEWS.md

@@ -10,21 +10,21 @@
 * Expanded test coverage with `test-gam_utils.R`.
 * Repository migrated: development moved from personal branches to [CSOgroup/SelectSim](https://github.com/CSOgroup/SelectSim); `dev` branch merged into `main` for initial public release.
 * Bumped version to 0.1.6 across all source files
-* Updated citation (`inst/CITATION`, `README`) to the published Nature Genetics article: Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi:10.1038/s41588-026-02661-4
+* Updated citation (`inst/CITATION`, `README`) to the published Nature Genetics article: Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. DOI: 10.1038/s41588-026-02661-4
 
 # SelectSim 0.0.1.3
 
 * Added a `NEWS.md` file to track changes to the package.
-* Rename the pacakge SelectSim to SelectSim by creating a new git folder.
-* Create CSO group repositroy and move the code there.
-* Created the website for github
+* Renamed the package to SelectSim by creating a new Git repository.
+* Created the CSOgroup repository and moved the code there.
+* Created the GitHub website.
 
 # SelectSim 0.0.1.4
 
-* Added Mijan in author's list
-* Remove C/C++ code dependecny to avoid installation diffculties in different systems.
-  * Hence move to using `Matrix` library functions and removed `RCpp` functions and code.
-* Update the website and vignette accordingly. 
+* Added Mijan to the author list.
+* Removed the C/C++ code dependency to avoid installation difficulties across systems.
+  * Moved to `Matrix` package functions and removed the `Rcpp` functions and compiled code.
+* Updated the website and vignette accordingly. 
 
 # SelectSim 0.0.1.5
 

R/data.R

@@ -1,6 +1,6 @@
 #' Lung adenocarcinoma from TCGA cohort as SelectSim run object
 #'
-#' Pre-processed TCGA LUAD data ready to pass directly to \code{selectX()}.
+#' Preprocessed TCGA LUAD data ready to pass directly to \code{selectX()}.
 #'
 #' @docType data
 #' @keywords datasets
@@ -22,6 +22,13 @@
 #'   \item{alteration.class}{Named character vector of alteration-type annotations
 #'     (length = number of genes). Names are gene symbols.}
 #' }
+#'
+#' @return A named list containing preprocessed LUAD input data for
+#'   \code{selectX()}.
+#' @examples
+#' data(luad_run_data)
+#' names(luad_run_data)
+#' str(luad_run_data, max.level = 1)
 NULL
 
 
@@ -34,7 +41,13 @@ NULL
 #' @keywords datasets
 #' @name luad_result
 #' @usage data(luad_result)
-#' @format A dataframe
+#' @format A data frame
+#'
+#' @return A data frame containing SelectSim results for the LUAD cohort.
+#' @examples
+#' data(luad_result)
+#' dim(luad_result)
+#' head(luad_result)
 NULL
 
 
@@ -48,7 +61,13 @@ NULL
 #' @keywords datasets
 #' @name luad_maf
 #' @usage data(luad_maf)
-#' @format A dataframe
+#' @format A data frame
+#'
+#' @return A data frame containing TCGA LUAD mutation data.
+#' @examples
+#' data(luad_maf)
+#' dim(luad_maf)
+#' head(luad_maf)
 NULL
 
 
@@ -62,6 +81,12 @@ NULL
 #' @name oncokb_genes
 #' @usage data(oncokb_genes)
 #' @format A list
+#'
+#' @return An object containing cancer-associated genes annotated by OncoKB.
+#' @examples
+#' data(oncokb_genes)
+#' length(oncokb_genes)
+#' head(oncokb_genes)
 NULL
 
 
@@ -75,6 +100,12 @@ NULL
 #' @name oncokb_truncating_genes
 #' @usage data(oncokb_truncating_genes)
 #' @format A list
+#'
+#' @return An object containing genes considered for truncating-mutation analyses.
+#' @examples
+#' data(oncokb_truncating_genes)
+#' length(oncokb_truncating_genes)
+#' head(oncokb_truncating_genes)
 NULL
 
 
@@ -87,5 +118,11 @@ NULL
 #' @keywords datasets
 #' @name variant_catalogue
 #' @usage data(variant_catalogue)
-#' @format A dataframe
-NULL
+#' @format A data frame
+#'
+#' @return A data frame containing cancer-gene and variant annotations.
+#' @examples
+#' data(variant_catalogue)
+#' dim(variant_catalogue)
+#' head(variant_catalogue)
+NULL

R/gam_utils.r

@@ -12,6 +12,9 @@
 #' Mutation list object
 #'
 #' @export
+#' @return A list containing the supported mutation-type classifications.
+#' @examples
+#' str(mutation_type)
 mutation_type <- list(
   "truncating" = c("Nonsense_Mutation", "Frame_Shift_Ins", "Frame_Shift_Del", "Splice_Site", "In_Frame_Ins", "In_Frame_Del"),
   "missense" = c("Missense_Mutation", "Splice_Site"),
@@ -22,6 +25,9 @@ mutation_type <- list(
 #' TCGA_maf_schema: schema for TCGA maf file to process the mutations
 #'
 #' @export
+#' @return A list defining the expected TCGA MAF column schema.
+#' @examples
+#' str(TCGA_maf_schema)
 TCGA_maf_schema <- list(
   "name" = "TCGA_maf",
   "column" = list(
@@ -43,6 +49,9 @@ TCGA_maf_schema <- list(
 #' GENIE_maf_schema: schema for GENIE maf file to process the mutations
 #'
 #' @export
+#' @return A list defining the expected GENIE MAF column schema.
+#' @examples
+#' str(GENIE_maf_schema)
 GENIE_maf_schema <- list(
   "column" = list(
     "gene" = "Hugo_Symbol",
@@ -69,8 +78,8 @@ GENIE_maf_schema <- list(
 #' @param maf a maf as dataframe
 #' @param values a list containing the elements to filter
 #' @param column column in maf file to filter
-#' @param inclusive a boolena to include or exclude the dataframe with values in list provided
-#' @param fixed a grep argument to specify if grep use the argumnet as string or not
+#' @param inclusive a boolean to include or exclude the data frame with values in list provided
+#' @param fixed a grep argument to specify if grep use the argument as string or not
 #' @param ... Other options
 #' @return filtered_maf  a filtered maf file
 #'
@@ -219,7 +228,7 @@ filter_maf_mutations <- function(maf, values, maf.col = c("Hugo_Symbol", "HGVSp_
 #' `filter_maf_schema()` takes a maf file and filters a MAF dataframe by retaining only the rows with a column value included in the values list
 #'
 #' @param maf a maf as dataframe
-#' @param schema a schema of datafrane check Select::TCGA_maf_schema for example
+#' @param schema a data-frame schema; see `TCGA_maf_schema` for an example
 #' @param column column in maf file to filter
 #' @param values a list containing the elements to file
 #' @param ... Other options
@@ -246,7 +255,7 @@ filter_maf_schema <- function(maf, schema = TCGA_maf_schema, column, values, ...
 #' `filter_maf_truncating()` takes a maf file and filters a MAF dataframe by retaining only the rows with a column value included in the values list
 #'
 #' @param maf a maf as dataframe
-#' @param schema a schema of datafrane check Select::TCGA_maf_schema for example
+#' @param schema a data-frame schema; see `TCGA_maf_schema` for an example
 #' @param ... Other options
 #' @return filtered_maf  a filtered maf file
 #'
@@ -269,7 +278,7 @@ filter_maf_truncating <- function(maf, schema = TCGA_maf_schema, ...) {
 #' `filter_maf_missense()` takes a maf file and filters a MAF dataframe by retaining only the rows with a column value included in the values list
 #'
 #' @param maf a maf as dataframe
-#' @param schema a schema of datafrane check Select::TCGA_maf_schema for example
+#' @param schema a data-frame schema; see `TCGA_maf_schema` for an example
 #' @param ... Other options
 #' @return filtered_maf  a filtered maf file
 #'
@@ -292,7 +301,7 @@ filter_maf_missense <- function(maf, schema = TCGA_maf_schema, ...) {
 #' `filter_maf_ignore()` takes a maf file and filters a MAF dataframe by retaining only the rows with a column value included in the values list
 #'
 #' @param maf a maf as dataframe
-#' @param schema a schema of datafrane check Select::TCGA_maf_schema for example
+#' @param schema a data-frame schema; see `TCGA_maf_schema` for an example
 #' @param ... Other options
 #' @return filtered_maf  a filtered maf file
 #'
@@ -317,7 +326,7 @@ filter_maf_ignore <- function(maf, schema = TCGA_maf_schema, ...) {
 #' `stat_maf_column()` takes a maf file and filters a MAF dataframe by retaining only the rows with a column value included in the values list
 #'
 #' @param maf a maf as dataframe
-#' @param column a schema of datafrane check Select::TCGA_maf_schema for example
+#' @param column a data-frame schema; see `TCGA_maf_schema` for an example
 #' @param ... Other options
 #' @return filtered_maf  a filtered maf file
 #'
@@ -386,7 +395,11 @@ stat_maf_gene <- function(maf, column = "Hugo_Symbol", ...) {
 #'
 #' @examples
 #' data(luad_maf, package = "SelectSim")
-#' gam <- maf2gam(luad_maf)
+#' small_maf <- luad_maf[
+#'   luad_maf$Tumor_Sample_Barcode %in%
+#'     unique(luad_maf$Tumor_Sample_Barcode)[1:5],
+#' ]
+#' gam <- maf2gam(small_maf)
 #' dim(gam)
 #'
 #' @export

R/selectX_create.r

@@ -273,7 +273,7 @@ generateW_mean_tmb <- function(tmb,
   if (!discrete) {
     w <- 1 / (1 + lambda * (tmb.FC - tau))
   }
-  W <- matrix(rep(w, ngenes), nrow = ngenes, byrow = T)
+  W <- matrix(rep(w, ngenes), nrow = ngenes, byrow = TRUE)
   return(W)
 }
 

R/selectX_run.R

@@ -6,7 +6,7 @@
 # Notes:
 # - Better Error message and running text
 # - Edge case: When sample size in less than 2 there is error in computation (need to fix a number to do this analysis)
-# - parallel::makeCluster(2, setup_strategy = "sequential") a possible fix to remove the erorr of not able to connect problem (https://github.com/rstudio/rstudio/issues/6692)
+# - parallel::makeCluster(2, setup_strategy = "sequential") a possible fix to remove the error of connection problem (https://github.com/rstudio/rstudio/issues/6692)
 # - Try to fix the parallel processing issuses
 ###
 
@@ -27,7 +27,7 @@
 #' @param sample.class sample covariates as named list.
 #' @param alteration.class alteration covariates as named list.
 #' @param n.cores no of cores.
-#' @param min.freq number of samples for features to be atleast mutated in.
+#' @param min.freq number of samples for features to be at least mutated in.
 #' @param n.permut number of simulations.
 #' @param lambda lambda parameter.
 #' @param tau tau (fold change) parameter.

R/selectX_stats.r

@@ -607,7 +607,7 @@ interaction.table <- function(al,
       )
     }
   }
-  results <- results[order(abs(results$nES), decreasing = T), ]
+  results <- results[order(abs(results$nES), decreasing = TRUE), ]
   results$type <- rep("ME", nrow(results))
   results$type[results$nES > 0] <- "CO"
   results$FDR <- results$nFDR2 <= maxFDR

README.Rmd

@@ -28,7 +28,7 @@ The method accounts for heterogeneous tumor types, tissue specificities, and dis
 
 This package accompanies the manuscript:
 
-> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
+> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. DOI: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 ## Installation
 
@@ -78,7 +78,7 @@ Full documentation and vignettes are available at <https://csogroup.github.io/Se
 
 If you use SelectSim in your research, please cite:
 
-> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. doi: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
+> Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. DOI: [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 You can also run `citation("SelectSim")` inside R for a formatted reference.
 

README.md

@@ -30,7 +30,7 @@ This package accompanies the manuscript:
 
 > Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).
 > Evolving patterns of co-mutations from tumor initiation to metastatic
-> progression. *Nature Genetics*. doi:
+> progression. *Nature Genetics*. DOI:
 > [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 ## Installation
@@ -44,7 +44,7 @@ pak::pak("CSOgroup/SelectSim")
 ```
 
 For more details on installation refer to
-[INSTALLATION](INSTALLATION.md).
+[INSTALLATION](https://github.com/CSOgroup/SelectSim/blob/main/INSTALLATION.md).
 
 ## Quick start
 
@@ -86,7 +86,7 @@ If you use SelectSim in your research, please cite:
 
 > Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026).
 > Evolving patterns of co-mutations from tumor initiation to metastatic
-> progression. *Nature Genetics*. doi:
+> progression. *Nature Genetics*. DOI:
 > [10.1038/s41588-026-02661-4](https://doi.org/10.1038/s41588-026-02661-4)
 
 You can also run `citation("SelectSim")` inside R for a formatted

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.

inst/WORDLIST

@@ -0,0 +1,38 @@
+ALS
+AMS
+CMD
+CSOgroup
+EDs
+LUAD
+MAF
+Mijan
+Missense
+NOTEs
+Nanni
+OncoKB
+Pre
+SFE
+SelectX
+Sesia
+TCGA
+TMB
+TMBs
+al
+coloured
+exclusivities
+gam
+gams
+ggplot
+grey
+hotspot
+labelled
+maf
+missense
+ngenes
+oncokb
+penalise
+selectX
+specificities
+tmb
+tmbs
+walkthrough