diff --git a/DESCRIPTION b/DESCRIPTION index a011339f3..f99ee8362 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -51,7 +51,6 @@ Imports: readxl, rlang, stringr, - S4Vectors, tidyverse, tidyr, tibble, @@ -69,6 +68,7 @@ Suggests: pROC, plyr, rmarkdown, + S4Vectors, testthat, prolfquaData, SummarizedExperiment, diff --git a/NAMESPACE b/NAMESPACE index 0ecaad0b7..feb286be9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -196,7 +196,6 @@ import(ggplot2) import(tidyverse) importFrom(GGally,ggpairs) importFrom(MASS,rlm) -importFrom(S4Vectors,SimpleList) importFrom(conflicted,conflict_prefer) importFrom(dplyr,all_of) importFrom(dplyr,anti_join) diff --git a/R/A_dataset_docu.R b/R/A_dataset_docu.R index 5a195ade2..424d6abd3 100644 --- a/R/A_dataset_docu.R +++ b/R/A_dataset_docu.R @@ -28,7 +28,6 @@ #' @importFrom stats na.omit p.adjust pbeta power.t.test prcomp predict pt qt quantile sd setNames sigma terms update vcov #' @importFrom stringr str_trim #' @import tidyverse -#' @importFrom S4Vectors SimpleList #' @importFrom utils combn data head read.csv tail unzip #' @importFrom yaml write_yaml NULL diff --git a/R/LFQData.R b/R/LFQData.R index c7b519748..491ef4530 100644 --- a/R/LFQData.R +++ b/R/LFQData.R @@ -1193,7 +1193,7 @@ LFQDataToSummarizedExperiment <- function(lfqdata){ wide <- lfqdata$to_wide(as.matrix = TRUE) ann <- data.frame(wide$annotation) rownames(ann) <- wide$annotation$sampleName - se <- SummarizedExperiment::SummarizedExperiment(SimpleList(LFQ = wide$data), colData = ann) + se <- SummarizedExperiment::SummarizedExperiment(S4Vectors::SimpleList(LFQ = wide$data), colData = ann) return(se) } }