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minor vignette fixes + contributors
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assaron committed Aug 13, 2024
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2 changes: 2 additions & 0 deletions DESCRIPTION
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Expand Up @@ -4,6 +4,8 @@ Version: 1.31.3
Authors@R: c(person("Gennady", "Korotkevich", role = "aut"),
person("Vladimir", "Sukhov", role = "aut"),
person("Nikolay", "Budin", role = "ctb"),
person("Nikita", "Gusak", role = "ctb"),
person("Zieman", "Mark", role = "ctb"),
person("Alexey", "Sergushichev", email = "[email protected]", role = c("aut", "cre")))
Description: The package implements an algorithm for fast gene set enrichment
analysis. Using the fast algorithm allows to make more permutations and get
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8 changes: 4 additions & 4 deletions vignettes/fgsea-tutorial.Rmd
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Expand Up @@ -164,14 +164,14 @@ head(fgseaRes)
enrichment tests, based on the hypergeometric test.

`fora` requires a foreground set of genes of interest, a background set consisting of all
robustly detected genes, and some pathways.
robustly detected genes (also called universe), and some pathways.

In the following example, the foreground (`fg`) consists of the 500 genes with the highest
`stat` value.

```{r}
fg <- names(head(exampleRanks[order(-exampleRanks)],500))
fg <- names(head(exampleRanks[order(exampleRanks, decreasing=TRUE)],500))
bg <- names(exampleRanks)
ora <- fora(genes=fg, universe=bg, pathways=examplePathways)
head(ora)
foraRes <- fora(genes=fg, universe=bg, pathways=examplePathways)
head(foraRes)
```

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