diff --git a/DESCRIPTION b/DESCRIPTION index 2fcfd65..06e7a82 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,7 +19,8 @@ Imports: cowplot, parallel, RcppNumerical, survey, - viridisLite + viridisLite, + BiocSet Description: Complex hypothesis testing through conditional cumulative distribution function estimation. Method is detailed in: Gauthier M, Agniel D, Ba Kalidou, Thiebaut R & Hejblum BP (2020). "Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis", BioRxiv . diff --git a/R/cit_gsa.R b/R/cit_gsa.R index 9dd0619..674ddca 100644 --- a/R/cit_gsa.R +++ b/R/cit_gsa.R @@ -15,6 +15,13 @@ #'test upon. Multiple covariates (\code{q>1}) are only supported by the #'asymptotic test. #' +#'#'@param geneset a vector, a gmt file or a BiocSet object. +#'If the parameter is \itemize{ +#' \item a vector : corresponds to the gene index in the matrix \code{M} +#' \item a gmt file : the genes names of each genes set in the file must be the same as those of the columns of the matrix M +#' \item a BiocSet object : the genes names of each genes set in the object must be the same as those of the columns of the matrix M +#'} +#' #'@param test a character string indicating whether the \code{'asymptotic'} or #'the \code{'permutation'} test is computed. #'Default is \code{'asymptotic'}. @@ -53,13 +60,6 @@ #' #'@param number_y an integer value indicating the number of y thresholds (and therefore #'the number of regressions) to perform the test. Default is 10. -#' -#'@param geneset a vector, a gmt file or a BiocSet object. -#'If the parameter is \itemize{ -#' \item a vector : corresponds to the gene index in the matrix \code{M} -#' \item a gmt file : the genes names of each genes set in the file must be the same as those of the columns of the matrix M -#' \item a BiocSet object : the genes names of each genes set in the object must be the same as those of the columns of the matrix M -#'} #' #'@return A list with the following elements:\itemize{ #' \item \code{which_test}: a character string carrying forward the value of