CalculatePValues: Calculate p-values for all edges in the network using a...

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Calculate p-values for all edges in the network using a Wilcoxon two-sample test for each edge.

Description

Calculate p-values for all edges in the network using a Wilcoxon two-sample test for each edge.

Usage

CalculatePValues(
  network,
  nullDistribution,
  pValueChunks = 100,
  doFDRAdjustment = TRUE,
  pValueFile = "pvalues.RDS",
  verbose = FALSE
)

Arguments

network	A combination of PANDA-like networks, with the following format (e.g., 3 networks), provided as a data frame: tf,gene,score1,score2,score3
nullDistribution	The null distribution, specified as a vector of values.
pValueChunks	The number of chunks to split when calculating the p-value. This parameter allows the edges to be split into chunks to prevent memory errors.
doFDRAdjustment	Whether or not to perform FDR adjustment.
pValueFile	The file where the p-values should be saved. If NULL, they are not saved and need to be recalculated.
verbose	Whether or not to print detailed information about the run.

Value

A vector of p-values, one for each edge.

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.