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Fix some typos. #20

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Fix some typos. #20

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4 changes: 2 additions & 2 deletions R/enrichR_functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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{
Expand Down Expand Up @@ -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{
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2 changes: 1 addition & 1 deletion man/plot_gsea.Rd
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2 changes: 1 addition & 1 deletion man/test_gsea.Rd
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4 changes: 2 additions & 2 deletions vignettes/DEP.Rmd
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Expand Up @@ -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
Expand Down Expand Up @@ -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")
Expand Down