diff --git a/DESCRIPTION b/DESCRIPTION index dc4ff34b..7516e043 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,7 +30,7 @@ LinkingTo: Rcpp, RcppEigen License: MIT + file LICENSE Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.3 BugReports: https://github.com/campbio/celda/issues biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian, ImmunoOncology, DataImport NeedsCompilation: yes diff --git a/R/splitModule.R b/R/splitModule.R index 8f7a5184..5b1462ae 100644 --- a/R/splitModule.R +++ b/R/splitModule.R @@ -5,13 +5,13 @@ #' @param x A \linkS4class{SingleCellExperiment} object #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. +#' @param module Integer. The module to be split. #' @param useAssay A string specifying which \link{assay} #' slot to use for \code{x}. Default "counts". #' @param altExpName The name for the \link{altExp} slot -#' to use. Default "featureSubset". -#' @param module Integer. The module to be split. +#' to use. Default \code{"featureSubset"}. #' @param n Integer. How many modules should \code{module} be split into. -#' Default 2. +#' Default \code{2}. #' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility, #' a default value of 12345 is used. If NULL, no calls to #' \link[withr]{with_seed} are made. @@ -21,9 +21,9 @@ #' @export setGeneric("splitModule", function(x, + module, useAssay = "counts", altExpName = "featureSubset", - module, n = 2, seed = 12345) { @@ -39,9 +39,9 @@ setGeneric("splitModule", #' @export setMethod("splitModule", signature(x = "SingleCellExperiment"), function(x, + module, useAssay = "counts", altExpName = "featureSubset", - module, n = 2, seed = 12345) { diff --git a/man/splitModule.Rd b/man/splitModule.Rd index 213efdf1..f9c7ec56 100644 --- a/man/splitModule.Rd +++ b/man/splitModule.Rd @@ -7,18 +7,18 @@ \usage{ splitModule( x, + module, useAssay = "counts", altExpName = "featureSubset", - module, n = 2, seed = 12345 ) \S4method{splitModule}{SingleCellExperiment}( x, + module, useAssay = "counts", altExpName = "featureSubset", - module, n = 2, seed = 12345 ) @@ -28,16 +28,16 @@ splitModule( with the matrix located in the assay slot under \code{useAssay}. Rows represent features and columns represent cells.} +\item{module}{Integer. The module to be split.} + \item{useAssay}{A string specifying which \link{assay} slot to use for \code{x}. Default "counts".} \item{altExpName}{The name for the \link{altExp} slot -to use. Default "featureSubset".} - -\item{module}{Integer. The module to be split.} +to use. Default \code{"featureSubset"}.} \item{n}{Integer. How many modules should \code{module} be split into. -Default 2.} +Default \code{2}.} \item{seed}{Integer. Passed to \link[withr]{with_seed}. For reproducibility, a default value of 12345 is used. If NULL, no calls to