diff --git a/R/enrichR_functions.R b/R/enrichR_functions.R index 9f31e6f..a488935 100644 --- a/R/enrichR_functions.R +++ b/R/enrichR_functions.R @@ -31,7 +31,7 @@ #' imputed <- impute(norm, fun = "MinProb", q = 0.01) #' #' # Test for differentially expressed proteins -#' diff <- diff <- test_diff(imputed, "control", "Ctrl") +#' diff <- test_diff(imputed, "control", "Ctrl") #' dep <- add_rejections(diff, alpha = 0.05, lfc = 1) #' #' \dontrun{ @@ -222,7 +222,7 @@ test_gsea <- function(dep, #' imputed <- impute(norm, fun = "MinProb", q = 0.01) #' #' # Test for differentially expressed proteins -#' diff <- diff <- test_diff(imputed, "control", "Ctrl") +#' diff <- test_diff(imputed, "control", "Ctrl") #' dep <- add_rejections(diff, alpha = 0.05, lfc = 1) #' #' \dontrun{ diff --git a/man/plot_gsea.Rd b/man/plot_gsea.Rd index ea79010..9fe59b8 100644 --- a/man/plot_gsea.Rd +++ b/man/plot_gsea.Rd @@ -57,7 +57,7 @@ norm <- normalize_vsn(filt) imputed <- impute(norm, fun = "MinProb", q = 0.01) # Test for differentially expressed proteins -diff <- diff <- test_diff(imputed, "control", "Ctrl") +diff <- test_diff(imputed, "control", "Ctrl") dep <- add_rejections(diff, alpha = 0.05, lfc = 1) \dontrun{ diff --git a/man/test_gsea.Rd b/man/test_gsea.Rd index 4602392..c1f3f76 100644 --- a/man/test_gsea.Rd +++ b/man/test_gsea.Rd @@ -46,7 +46,7 @@ norm <- normalize_vsn(filt) imputed <- impute(norm, fun = "MinProb", q = 0.01) # Test for differentially expressed proteins -diff <- diff <- test_diff(imputed, "control", "Ctrl") +diff <- test_diff(imputed, "control", "Ctrl") dep <- add_rejections(diff, alpha = 0.05, lfc = 1) \dontrun{ diff --git a/vignettes/DEP.Rmd b/vignettes/DEP.Rmd index fe6a2fd..4791a10 100644 --- a/vignettes/DEP.Rmd +++ b/vignettes/DEP.Rmd @@ -119,7 +119,7 @@ Additionally, some proteins do not have an annotated gene name and for those we data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";") # Are there any duplicated names? -data$name %>% duplicated() %>% any() +data_unique$name %>% duplicated() %>% any() ``` ## Generate a SummarizedExperiment object @@ -274,7 +274,7 @@ For the contrasts generation, the control sample has to be specified. Additionally, the types of contrasts to be produced need to be indicated, allowing the generation of all possible comparisons ("all") or the generation of contrasts of every sample versus control ("control"). Alternatively, the user can manually specify the contrasts to be tested (type = "manual"), which need to be specified in the argument _test_. ``` {r statistics} -# Differential enrichment analysis based on linear models and empherical Bayes statistics +# Differential enrichment analysis based on linear models and empirical Bayes statistics # Test every sample versus control data_diff <- test_diff(data_imp, type = "control", control = "Ctrl")