artmsEnrichLog2fc {artMS} | R Documentation

## Enrichment of changes in protein abundance or PTMs

### Description

Enrichment analysis of the selected proteins

### Usage

    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

    # 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))

[Package artMS version 1.6.5 Index]