analyzeNetCat: Performs significant testing of each edge in the network for...

In SystemsGenetics/KINC.R: Provides additional functions for network files created using KINC.

Description

Performs significant testing of each edge in the network for a set of annotation categories.

Usage

analyzeNetCat(
  net,
  osa,
  ematrix,
  field,
  test = "binomial",
  correction = "hochberg",
  progressBar = TRUE,
  category = NA,
  t1_psucc = 0.25,
  t2_psucc = 0.75
)

Arguments

net	A network data frame containing the KINC-produced network. The loadNetwork function imports a dataframe in the correct format for this function.
osa	The ordered sample annotation data frame.
ematrix	The expression matrix data frame.
field	The field in the osa variable on which enrichment will be performed.
test	The statistical test to perform. This is 'fishers' for an enrichment test.
progressBar	Set to FALSE to repress progress bar
category	By default this function will cylce through all categories of the 'field' argument. But to limit the analysis to just one category set it here.
t1_psucc	For the bionomial test only. The probabilty of success for the first binomial test. This value indicates the percentage of samples in the cluster that must belong to the category.
t2_psucc	For the binomial test only. The probability of success for the second binomial test. This value indicates the percentage of category samples that must belong to the cluster.
correction.	The method to apply for multiple testing correction. Valid values are identical to those available to the p.adjust function. The default is to apply 'hochberg' correction.
nthreads	The number of threads (CPU cores/threads) used to analyze the network.

SystemsGenetics/KINC.R documentation built on Nov. 10, 2021, 9:22 p.m.