miRNAPathwayEnrichment: Enrichment Probability Of miRNAs

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

Enrichment Probability Of miRNAs

Description

Outputs enrichment probability of miRNAs based on pathway clusters.

Usage

miRNAPathwayEnrichment(
  mirSets,
  pathwaySets,
  geneSelection = NULL,
  mirSelection = NULL,
  fromID = "ENSEMBL",
  toID = "ENTREZID",
  minPathSize = 9,
  numCores = 1,
  outDir = ".",
  saveOutName = NULL
)

Arguments

mirSets	Table of miRNAs and a list of their interactions with genes in ENTREZ ID.
pathwaySets	Table of pathways and a list of their interactions with genes in ENTREZ ID.
geneSelection	Table of genes with dtype; if not NULL, select only genes from a given table.
mirSelection	Table of miRNA names; if not NULL, select only miRNAs from given table.
fromID	ID of genes in geneSelection.
toID	ID of genes used in pcxn and pathways set.
minPathSize	Filter out pathways with sets less than given value.
numCores	Number of CPU cores to use, must be at least one.
outDir	Output directory.
saveOutName	If not NULL, saves output as RDS using save name.

Value

Table of enrichment, each row contains mirna-pathway and its enrichment p-values.

Examples

data(msigdb_c2)
data(targetScan_03)
miRNAPathwayEnrichment(targetScan_03[1:20],msigdb_c2[1:20])

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