benchmarkNetwork: Benchmarks a Network against a Reference Network/Interaction...

In heuselm/mocode: Integrates MS-based-proteomics Data Analysis Code

Benchmarks a Network against a Reference Network/Interaction set

Description

Benchmarks a Network against a Reference Network/Interaction set

Usage

benchmarkNetwork(
  Network,
  Reference = "intact.txt",
  names_net = c("UniprotA", "UniprotB"),
  scores_net = c("pW", "pNI", "pInt"),
  names_ref = c("uniprot_a", "uniprot_b", "miscore"),
  minscore_ref = 0.5,
  n_shuffle_iter = 10,
  output = "pdf_csv"
)

Arguments

Network	data.table or path to tab-separated .txt file or data.table with columns uniprot_a uniprot_b and confidence score
Reference	Reference table, data.table or path to tab-separated text with headers containing info uniprot_a and uniprot_b for true interactions. Can also point to data.table with this information structure.
names_net	Character vector specifiying the column names in Network containing the uniprot identifiers a and b and the confidence score. Defaults to c("uniprot_a", "uniprot_b")
scores_net	Character vector of score column names in the network data. Defaults to the Bioplex scores c("pW", "pNI", "pInt").
names_ref	Character vector specifiying the column names in Network containing the uniprot identifiers a and b and the confidence score. Defaults to c("uniprot_a", "uniprot_b" , "score")
minscore_ref	minimum score threshold in the reference.
n_shuffle_iter	Number of shufflings to generate the negative test set.
output	Character string, wether .pdfs and .csvs shall be written to working folder or whether the output should go to Rconsole. Options are "pdf_csv" or "Rconsole" with default "pdf_csv".

Value

data.frame with column headers as defined by arg protcolnames and cor_pearson and cor_spearman

heuselm/mocode documentation built on Oct. 23, 2023, 8:43 a.m.