permute_pdr: Create a permuted network

Description Usage Arguments Value Author(s)

View source: R/AbHAC.R

Description

Used inside the fisher exact test motor function, it will provide permuted networks for estimating FDR/FWER.

Usage

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permute_pdr(ppi.database, df_pr_freq, method = "AsPaper", k = 4,
  verbose = FALSE)

Arguments

ppi.database

2 column undirected protein interaction network

df_pr_freq

dataframe of first column as unique protein names of ppi.database, and 2nd column as number of times they have occured in the network. This is calculated by get_edgedegree_freq

method

Specify "equal" for equal number of proteins in each bin sorted by edge degree, "ByDegree" to create bins solely based on edge degree and "AsPaper" to have one bin for each edge degree unless the number of proteins in the edge degree is lower than 3. For such proteins create k equal size bins.

k

number of bins to divide the proteins and permute inside those bins

Value

ppi_permuted 2 column undirected protein interaction network

Author(s)

Mehran Karimzadeh mehran.karimzadehreghbati at mail dot mcgill dot ca


mehrankr/AbHAC documentation built on May 22, 2017, 3:28 a.m.