Enrichment of changes in protein abundance or PTMs — artmsEnrichLog2fc • artMS
Description: Enrichment analysis of the selected proteins

# Enrichment of changes in protein abundance or PTMs

Source: `R/enrichments.R`
`artmsEnrichLog2fc.Rd`

Enrichment analysis of the selected proteins

    artmsEnrichLog2fc(
      dataset,
      species,
      background,
      heatmaps = FALSE,
      output_name = "enrichment.txt",
      verbose = TRUE
    )

## Arguments

dataset | (data.frame) with a `Gene` and `Comparison or Label` (with the name of the comparisons specified in the contrast file) columns
species | (char) Specie, only supported "human" or "mouse"
background | (vector) Background genes for the enrichment analysis.
heatmaps | (logical) if `TRUE` generates heatmaps (pdf), `FALSE` (default) otherwise.
output_name | (char) Name of the annotation files, which will be used as well for the heatmaps (if `heatmaps` is selected) Default `output_name = "enrichment.txt"`
verbose | (logical) `TRUE` (default) shows function messages

## Value

(data.frame) Results from the enrichment analysis using Gprofiler and heatmaps (if selected)

## Examples

    if (FALSE) {
    # The data must be annotated (Protein and Gene columns)
    data_annotated <- artmsAnnotationUniprot(
                          x = artms_data_ph_msstats_results,
                          columnid = "Protein",
                          species = "human")
    # And then the enrichment
    enrich_set <- artmsEnrichLog2fc(
                       dataset = data_annotated,
                       species = "human",
                       background = unique(data_annotated$Gene))
    }