bngenetest: bngenetest

In noriakis/CBNplot: plot bayesian network inferred from gene expression data based on enrichment analysis results

bngenetest

Description

Testing various R for bayesian network between genes

Usage

bngenetest(
  results,
  exp,
  expSample = NULL,
  algo = "hc",
  Rrange = seq(2, 40, 2),
  cl = NULL,
  algorithm.args = NULL,
  pathNum = NULL,
  convertSymbol = TRUE,
  expRow = "ENSEMBL",
  scoreType = "aic-g",
  orgDb = org.Hs.eg.db,
  bypassConverting = FALSE
)

Arguments

results	the enrichment analysis result
exp	gene expression matrix
expSample	candidate rows to be included in the inference default to all
algo	structure learning method used in boot.strength() default to "hc"
Rrange	the sequence of R values to be tested
cl	cluster object from parallel::makeCluster()
algorithm.args	parameters to pass to bnlearn structure learnng function
pathNum	the pathway number (the number of row of the original result, ordered by p-value)
convertSymbol	whether the label of resulting network is converted to symbol, default to TRUE
expRow	the type of the identifier of rows of expression matrix
scoreType	return the specified scores
orgDb	perform clusterProfiler::setReadable based on this organism database
bypassConverting	bypass symbol converting

Value

list of graphs and scores

Examples

data("exampleEaRes");data("exampleGeneExp")
res <- bngenetest(results = exampleEaRes, exp = exampleGeneExp,
algo="hc", Rrange=seq(10, 30, 10), pathNum=1, scoreType="bge")

noriakis/CBNplot documentation built on Oct. 10, 2024, 12:21 p.m.