get_Upset_list {mpwR}

Generate Upset list

Description

Generate a list as input for Upset plot

Usage

get_Upset_list(
  input_list,
  level = c("Precursor.IDs", "Peptide.IDs", "Protein.IDs", "ProteinGroup.IDs"),
  percentage_runs = 100,
  flowTraceR = FALSE,
  remove_traceR_unknownMods = FALSE
)

Arguments

input_list

A list with data frames and respective level information.

level

Character string. Choose between "Precursor.IDs", "Peptide.IDs", "Protein.IDs", "ProteinGroup.IDs". Default is "Precursor.IDs".

percentage_runs

Number. Percentage of appearance in runs. 100 means: Identification is present in 100% of runs. Default is 100.

flowTraceR

Logical. If FALSE no level conversion is applied. Useful for inter-software comparisons. Default is FALSE.

remove_traceR_unknownMods

Logical. If FALSE no unknown Modifications are filtered out. Only applies if flowTraceR is set to TRUE. Default is FALSE.

Details

An input is generated for Upset plotting for either precursor-, peptide-, protein- or proteingroup-level. For inter-software comparisons flowTraceR is integrated.

Value

This function returns a list for each analysis with respective level information.

Author(s)

Oliver Kardell

Examples

# Load libraries
library(tibble)
library(magrittr)
library(stringr)

# Example data
data <- list(
DIANN = list(
 filename = "B",
 software = "DIA-NN",
 data = list(
   "DIA-NN" = tibble::tibble(
     Run_mpwR = rep(c("A","B"), times = 10),
     Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
     Protein.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4),
     Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 4),
     ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 4)
   )
 )
),
Spectronaut = list(
 filename = "C",
 software = "Spectronaut",
 data = list(
   "Spectronaut" = tibble::tibble(
     Run_mpwR = rep(c("A","B"), times = 15),
     Precursor.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6),
     Peptide.IDs_mpwR = rep(c("A", "A", "B", "B", "C"), each = 6),
     ProteinGroup.IDs_mpwR = rep(c("A2", "A3", "B2", "B3", "C1"), each = 6)
   )
 )
)
)

# Result
output <- get_Upset_list(
  input_list = data,
  level = "Precursor.IDs"
)