bngenetest: bngenetest

bngenetestR Documentation

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.