calculate_treatment_enrichment: Check treatment enrichment

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

Check treatment enrichment

Description

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

Usage

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

Arguments

data	a data frame contains at least the input variables.
protein_id	a character column in the data data frame that contains the protein accession numbers.
is_significant	a logical column in the data data frame that indicates 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	a logical column in the data data frame that indicates if the corresponding protein binds to the treatment. This information can be obtained from different databases, e.g. UniProt.
treatment_name	a character value that indicates the treatment name. It will be included in the plot title.
plot	a logical value 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

# Create example data
data <- data.frame(
  protein_id = c(paste0("protein", 1:50)),
  significant = c(
    rep(TRUE, 20),
    rep(FALSE, 30)
  ),
  binds_treatment = c(
    rep(TRUE, 10),
    rep(FALSE, 10),
    rep(TRUE, 5),
    rep(FALSE, 25)
  )
)

# Plot treatment enrichment
calculate_treatment_enrichment(
  data,
  protein_id = protein_id,
  is_significant = significant,
  binds_treatment = binds_treatment,
  treatment = "Rapamycin",
  plot = TRUE
)

# Calculate treatment enrichment
enrichment <- calculate_treatment_enrichment(
  data,
  protein_id = protein_id,
  is_significant = significant,
  binds_treatment = binds_treatment,
  plot = FALSE
)

enrichment

protti documentation built on Jan. 22, 2023, 1:11 a.m.