merge_omics: merge.omics merges proteomics, genomics, and ligandomics data...
In IFIproteomics/E2Predictor:

merge.omics merges proteomics, genomics, and ligandomics data of an experiment

merge_omics(selected.cell.line, dbfile, is_perturbation = F,
  condition = NULL, additionalGrepCondition = "", minReplicates = 1,
  allele.predictions = NULL, allele.predictor = "ic50",
  nM.threshold = 1000, saveAllResults = F, GOcategories = NULL)

`selected.cell.line`	cell line to integrate data
`dbfile`	Uniprot database filename (NOT in fasta format! Use the xls format)
`is_perturbation`	indicates if the experiment is a perturbation experiment
`condition`	in case of a perturbation, this indicates which condition you want to use
`minReplicates`	for ligandomics data, the minimum number of biological replicates required to validate a ligand
`allele.predictions`	data frame containing allele predictions for the ligands. If NULL, they will be estimated
`allele.predictor`	c("rank", "ic50") predictor to be used.
`nM.threshold`	minimum nanomolar threshold for validating the predictions
`saveAllResults`	save allele predictions and merged omics table at the working directory
`GOcategories`	a string vector containing gene ontology categories you want to include as separate variables