diff --git a/R/cit_gsa.R b/R/cit_gsa.R index ed74532..5f2b629 100644 --- a/R/cit_gsa.R +++ b/R/cit_gsa.R @@ -15,7 +15,7 @@ #'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. +#' @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 diff --git a/man/ccdf.Rd b/man/ccdf.Rd index 4bb9c48..4800109 100644 --- a/man/ccdf.Rd +++ b/man/ccdf.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ccdf.R +% Please edit documentation in R/CCDF.R \name{ccdf} \alias{ccdf} \title{Estimate the empirical conditional cumulative distribution function} diff --git a/man/cit_gsa.Rd b/man/cit_gsa.Rd index c988c07..ef9c812 100644 --- a/man/cit_gsa.Rd +++ b/man/cit_gsa.Rd @@ -33,14 +33,7 @@ are only supported by the asymptotic test.} \item{Z}{a data frame of size \code{n x q} of numeric or factor vector(s) containing the covariate(s) to condition the independence 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 -}} +asymptotic test.} \item{test}{a character string indicating whether the \code{'asymptotic'} or the \code{'permutation'} test is computed. @@ -79,6 +72,13 @@ observed expression value is used as a distinct threshold. Default is \code{TRUE \item{number_y}{an integer value indicating the number of y thresholds (and therefore the number of regressions) to perform the test. Default is 10.} + +\item{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 +}} } \value{ A list with the following elements:\itemize{