phospho_input: Generate a clean phosphoproteomic file for NetworKIN and...
In gaelfortin/phosphogo: Analyze Your Phosphoproteomic Data

Description Usage Arguments

View source: R/phospho_input.R

This function imports, clean, and prepare phosphoproteomic data for NetworKIN and IV-KEA.

phospho_input(
  phospho_file = "phospho_human.xlsx",
  species = "hsa",
  phosphosites_column = "PhosphoSite",
  log2_column = "Log2",
  fdr_column = "Adj. Pvalue",
  output_folder = "myexperiment/"
)

`phospho_file`	`<.xlsx or .csv file>` Raw phosphoproteomic data
`species`	`<character>` Species code from which samples were obtained (`hsa` or `mmu`).
`phosphosites_column`	`<column_name>` Column with phosphosite names
`log2_column`	`<column_name>` Column with log2(experiment/control) values
`fdr_column`	`<column_name>` Column with adjusted pvalues
`output_folder`	`<character>` Where the output files should be stored (with a `/` at the end)