bnpathtest: bnpathtest

bnpathtestR Documentation

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.