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

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.