map_proteome: Map protein abundance using protein IDs or gene names

In VoisinneG/proteinRuler: proteinRuler

Map protein abundance using protein IDs or gene names

Description

Add protein abundance to an InteRactome. For multiple identifiers, the abundance of the first match in the proteome dataset is returned.

Usage

map_proteome(
  df,
  col_ID = "Protein.IDs",
  col_names = "names",
  sep_primary = NULL,
  sep_secondary = NULL,
  proteome_dataset,
  pdata_sep = ";",
  pdata_col_ID = "Protein.IDs",
  pdata_col_gene_name = "Gene.names",
  pdata_col_copy_number = "Copy.Number",
  map_gene_name = FALSE,
  return_indexes = FALSE,
  updateProgress = NULL
)

Arguments

df	a data.frame or a list
col_ID	column of df containing protein IDs
col_names	column of df containing gene names. Only used if map_gene_name = TRUE.
sep_primary	Separator between different proteins in df
sep_secondary	Set of separators used sequentially (from right to left) to identify protein IDs for each protein in df
proteome_dataset	Dataset containing protein abundances.
pdata_sep	Separator between different proteins in proteome_dataset
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 protein abundances
map_gene_name	logical, map protein using gene names rather than protein IDs
return_indexes	logical, return vector of matching indexes
updateProgress	used to display progress in shiny apps protein abundances (in log10)

Examples

names <- LETTERS
names[3] <- "Z;A"
copies <- runif(length(LETTERS), 0, 100)
proteome <- data.frame(names, copies, stringsAsFactors = FALSE)
names(proteome) <- c("Gene.names", "Copy.Number")
df <- data.frame("names" = c("C", "M", "Z", "A", "KL Z;A"))
res <- map_proteome(df, col_names = "names", proteome_dataset = proteome, map_gene_name = TRUE)

VoisinneG/proteinRuler documentation built on Oct. 13, 2022, 9:47 p.m.