perform_Fisher_exact_test: Perform Fisher exact test
In gaelfortin/phosphogo: Analyze Your Phosphoproteomic Data

Description Usage Arguments

View source: R/perform_fisher_exact_test.R

This function computes Fisher exact test and the corresponding adjusted p-values (FDR) for upregulated vs downregulated phosphosites, upregulated vs all phosphosites, downregulated vs all phosphosites.

perform_Fisher_exact_test(
  predictions_file = "networkin_output.csv",
  predictions = "networkin",
  output_folder = "myexperiment/",
  FC_threshold = 1.2
)

`predictions_file`	`<character>` Location of the file with top predictions per phosphosite
`predictions`	`<character>` The algorithm used for predictions (NetworKIN or IV-KEA)
`output_folder`	`<character>` Where the output files should be stored
`FC_threshold`	`<numeric>` Fold change threshold to select phosphosites.