prioritizeMicroRNA: Prioritize miRNA

In pouryany/PanomiR: Detection of miRNAs that regulate interacting groups of pathways

Prioritize miRNA

Description

Outputs a table of miRNA ordered with respective p-values derived from method for prioritization

Usage

prioritizeMicroRNA(
  enriches0,
  pathClust,
  method = "AggInv",
  methodThresh = NULL,
  enrichmentFDR = 0.25,
  topClust = 2,
  sampRate = 1000,
  outDir = ".",
  dataDir = ".",
  saveSampling = TRUE,
  runJackKnife = TRUE,
  saveJackKnife = FALSE,
  numCores = 1,
  saveCSV = TRUE,
  prefix = "",
  autoSeed = TRUE
)

Arguments

enriches0	miRNA-pathway enrichment dataset obtained from miRNAPathwayEnrichment.
pathClust	Pathway clusters, obtained from MappingPathwaysClusters.
method	Vector of methods pCut, AggInv, AggLog, sumz, sumlog.
methodThresh	Vector of methods threshold for each method in method, if NULL use default thresh values in method.
enrichmentFDR	FDR cut-off calculating miRNA-pathway hits in the input cluster based on significant enrichment readouts.
topClust	Top x clusters to perform miRNA prioritization on.
sampRate	Sampling rate for CLT.
outDir	Output directory.
dataDir	Data directory.
saveSampling	If TRUE, saves sampling data as RDS for each cluster in topClust in dataDir.
runJackKnife	If TRUE, jacknifing will be performed.
saveJackKnife	If TRUE, saves jack-knifed sampling data as RDS for each cluster in topClust in dataDir.
numCores	Number of CPU cores to use, must be at least one.
saveCSV	If TRUE, saves CSV file for each cluster in topClust in outDir.
prefix	Prefix for all saved data.
autoSeed	random permutations are generated based on predetermined seeds. TRUE will give identical results in different runs.

Value

Table of miRNA and p-values, each row contains a miRNA and its associated p-values from the methods.

Examples

data("miniTestsPanomiR")

prioritizeMicroRNA(enriches0 = miniTestsPanomiR$miniEnrich,
   pathClust = miniTestsPanomiR$miniPathClusts$Clustering,
   topClust = 1,
   sampRate = 50,
   method = c("aggInv"),
   saveSampling = FALSE,
   runJackKnife = FALSE,
   numCores = 1,
   saveCSV = FALSE)

pouryany/PanomiR documentation built on Aug. 20, 2022, 11:17 p.m.