@@ -1,6 +1,6 @@

 Package: Cepo

 Title: Cepo for the identification of differentially stable genes

-Version: 0.99.2

+Version: 0.99.3

 Authors@R: 

     c(

     person(given = "Hani Jieun",

@@ -51,4 +51,5 @@ Suggests:

     patchwork

 VignetteBuilder: knitr

 Depends: 

+    GSEABase,

     R (>= 4.1)

@@ -18,6 +18,14 @@ using the `remotes` package:

 remotes::install_github("PYangLab/Cepo")

 ```

+You can install the Bioconductor version of _Cepo_ from:

+

+``` r

+if (!requireNamespace("BiocManager", quietly = TRUE))

+    install.packages("BiocManager")

+BiocManager::install("Cepo")

+```

+

 To also build the vignettes use:

 ``` r

@@ -21,39 +21,54 @@ Cepo(

 )

 }

 \arguments{

-\item{exprsMat}{Expression matrix where columns denote cells and rows denote genes}

+\item{exprsMat}{Expression matrix where columns denote cells and rows

+denote genes}

 \item{cellTypes}{Vector of cell type labels}

-\item{minCells}{Integer indicating the minimum number of cells required within a cell type}

+\item{minCells}{Integer indicating the minimum number of cells required

+within a cell type}

-\item{minCelltype}{Integer indicating the minimum number of cell types required in each batch}

+\item{minCelltype}{Integer indicating the minimum number of cell types

+required in each batch}

-\item{exprsPct}{Percentage of lowly expressed genes to remove. Default to NULL to not remove any genes.}

+\item{exprsPct}{Percentage of lowly expressed genes to remove.

+Default to NULL to not remove any genes.}

-\item{logfc}{Numeric value indicating the threshold of log fold-change to use to filter genes.}

+\item{logfc}{Numeric value indicating the threshold of log fold-change

+to use to filter genes.}

-\item{computePvalue}{Whether to compute p-values using bootstrap test. Default to NULL to not make computations.

-Set this to an integer to set the number of bootstraps needed (recommend to be at least 100).}

+\item{computePvalue}{Whether to compute p-values using bootstrap test.

+Default to NULL to not make computations.

+Set this to an integer to set the number of bootstraps needed

+(recommend to be at least 100).}

-\item{variability}{A character indicating the stability measure (CV, IQR, MAD, SD). Default is set to CV.}

+\item{variability}{A character indicating the stability measure

+(CV, IQR, MAD, SD). Default is set to CV.}

-\item{method}{Character indicating the method for integration the two stability measures. By default this is set to "weightedMean" with eqaul weights.}

+\item{method}{Character indicating the method for integration

+the two stability measures. By default this is set to

+'weightedMean' with equal weights.}

-\item{weight}{Vector of two values indicating the weights for each stability measure. By default this value is c(0.5, 0.5).}

+\item{weight}{Vector of two values indicating the weights for each stability

+measure. By default this value is c(0.5, 0.5).}

-\item{workers}{Number of cores to use. Default to 1, which invokes \code{BiocParallel::SerialParam}.

-For workers greater than 1, see the \code{workers} argument in \code{BiocParallel::MulticoreParam} and \code{BiocParallel::SnowParam}.}

+\item{workers}{Number of cores to use. Default to 1, which invokes

+\code{BiocParallel::SerialParam}.

+For workers greater than 1, see the \code{workers} argument in

+\code{BiocParallel::MulticoreParam} and \code{BiocParallel::SnowParam}.}

 \item{block}{Vector of batch labels}

-\item{...}{Additional arguments passed to \code{BiocParallel::MulticoreParam} and \code{BiocParallel::SnowParam}.}

+\item{...}{Additional arguments passed to \code{BiocParallel::MulticoreParam}

+and \code{BiocParallel::SnowParam}.}

 }

 \value{

 Returns a list of key genes.

 }

 \description{

-ExprsMat accepts various matrix objects, including DelayedArray and HDF5Array for

+ExprsMat accepts various matrix objects,

+including DelayedArray and HDF5Array for

 out-of-memory computations. See vignette.

 }

 \examples{

@@ -7,10 +7,13 @@

 setCepoBPPARAM(workers = 1L, ...)

 }

 \arguments{

-\item{workers}{Number of cores to use. Default to 1, which invokes \code{BiocParallel::SerialParam}.

-For workers greater than 1, see the \code{workers} argument in \code{BiocParallel::MulticoreParam} and \code{BiocParallel::SnowParam}.}

+\item{workers}{Number of cores to use. Default to 1, which invokes

+\code{BiocParallel::SerialParam}.

+For workers greater than 1, see the \code{workers} argument in

+\code{BiocParallel::MulticoreParam} and \code{BiocParallel::SnowParam}.}

-\item{...}{Additional arguments passed to \code{BiocParallel::MulticoreParam} and \code{BiocParallel::SnowParam}.}

+\item{...}{Additional arguments passed to \code{BiocParallel::MulticoreParam}

+and \code{BiocParallel::SnowParam}.}

 }

 \value{

 Parameters for parallel computing depending on OS

@@ -33,8 +33,9 @@ citation("Cepo")

 ## Package installation

 The development version of *Cepo* can be installed with the following command:

 ```

-install.packages("remotes")

-remotes::install_github("PYangLab/Cepo")

+if (!requireNamespace("BiocManager", quietly = TRUE))

+    install.packages("BiocManager")

+BiocManager::install("Cepo")

 ```

 # Differential stability analysis using Cepo

@@ -255,8 +256,7 @@ library(escape)

 library(fgsea)

 hallmark <- getGeneSets(species = "Homo sapiens", 

                            library = "H")

-hallmarkList <- lapply([email protected], function(x) x@geneIds)

-names(hallmarkList) <- lapply([email protected], function(x) x@setName)

+hallmarkList <- geneIds(hallmark)

 fgseaRes <- fgsea(pathways = hallmarkList, 

                   stats    = sort(ds_res_batches$average$stats[,"beta"]),