Add protein abundance to an InteRactome

Source: R/Main_functions.R

Add protein abundance to an InteRactome. Protein abundance are obtained from CD4+ effector T cells.

merge_proteome(res, col_ID = "Protein.IDs", col_names = "names",
  sep_primary = ";", sep_secondary = c("|", "-"), proteome_dataset,
  pdata_col_ID = "Protein.ID", pdata_col_gene_name = "Gene.names",
  pdata_col_copy_number = "Copy.Number", map_gene_name = FALSE,
  updateProgress = NULL)

Arguments

res

an InteRactome
col_ID

name of res containing protein IDs
col_names

name of res containing gene names. Only used if map_gene_name = TRUE.
sep_primary

Separator between different proteins
sep_secondary

Set of separators used sequentially (from right to left) to identify protein IDs for each protein
proteome_dataset

Dataset containing protein abundances.
pdata_col_ID

column of proteome_dataset containing protein IDs
pdata_col_gene_name

column of proteome_dataset containing gene names
pdata_col_copy_number

column of proteome_dataset containing
map_gene_name

logical, map protein using gene names rather than protein IDs
updateProgress

used to display progress in shiny apps protein abundances (in log10)