analyzeEdgeCat: Performs significant testing of a single edge in the network...

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

Description

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

Usage

analyzeEdgeCat(
  i,
  osa,
  net,
  ematrix,
  field,
  test = "binomial",
  category = NA,
  t1_psucc = 0.25,
  t2_psucc = 0.75
)

Arguments

i	The index of the edge in the network
osa	The sample annotation matrix. One column must contain the header 'Sample' and the remaining colums correspond to an annotation type. The rows of the anntation columns should contain the annotations.
net	A network dataframe containing the KINC-produced network. The loadNetwork function imports a dataframe in the correct format for this function.
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: 'fishers' or 'binomial'
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.

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