artmsEnrichLog2fc: Enrichment of changes in protein abundance or PTMs

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

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

## Not run: 
# 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))

## End(Not run)

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.