bnpathtest: bnpathtest

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

bnpathtest

Description

Testing various R for bayesian network between pathways

Usage

bnpathtest(
  results,
  exp,
  expSample = NULL,
  algo = "hc",
  algorithm.args = NULL,
  expRow = "ENSEMBL",
  cl = NULL,
  orgDb = org.Hs.eg.db,
  bypassConverting = FALSE,
  qvalueCutOff = 0.05,
  adjpCutOff = 0.05,
  nCategory = 15,
  Rrange = seq(2, 40, 2),
  scoreType = "aic-g"
)

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"
algorithm.args	parameters to pass to bnlearn structure learnng function
expRow	the type of the identifier of rows of expression matrix
cl	cluster object from parallel::makeCluster()
orgDb	perform clusterProfiler::setReadable based on this organism database
bypassConverting	bypass symbol converting
qvalueCutOff	the cutoff value for qvalue
adjpCutOff	the cutoff value for adjusted pvalues
nCategory	the number of pathways to be included
Rrange	the sequence of R values to be tested
scoreType	return the specified scores

Value

list of graphs and scores

Examples

data("exampleEaRes");data("exampleGeneExp")
res <- bnpathtest(results = exampleEaRes, exp = exampleGeneExp,
       algo="hc", Rrange=seq(10, 30, 10), expRow = "ENSEMBL",
       scoreType="bge")

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