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

# 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))
#> ---+ Enrichment analysis using gProfiler...
#> done!
#> --- No significant results from the enrichment analysis