protti: treatment_enrichment – R documentation

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treatment_enrichment

Check treatment enrichment

Description

Check for an enrichment of proteins interacting with the treatment in significantly changing proteins as compared to all proteins.

Usage

treatment_enrichment(
  data,
  protein_id,
  is_significant,
  binds_treatment,
  treatment_name,
  plot = TRUE
)

Arguments

`data`	A dataframe contains at least the input variables.
`protein_id`	The name of the column containing the protein accession numbers.
`is_significant`	The name of the column containing a logical indicating if the corresponding protein has a significantly changing peptide. The input data frame may contain peptide level information with significance information. The function is able to extract protein level information from this.
`binds_treatment`	The name of the column containing a logical indicating if the corresponding protein binds to the treatment. This information can be obtained from different databases, e.g Uniprot.
`treatment_name`	A character vector of the treatment name. It will be included in the plot title.
`plot`	A logical indicating whether the result should be plotted or returned as a table.

Value

A bar plot displaying the percentage of all detect proteins and all significant proteins that bind to the treatment. A Fisher's exact test is performed to calculate the significance of the enrichment in significant proteins compared to all proteins. The result is reported as a p-value. If plot = FALSE a contingency table in long format is returned.

Examples

## Not run: 
treatment_enrichment(
  data,
  protein_id = pg_protein_accessions,
  is_significant = significant,
  binds_treatment = binds_metals,
  treatment = "Metals"
)

## End(Not run)

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release