find_miRNA_targets: The find_miRNA_targets function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The find_miRNA_targets function

Description

Detection potential target protein-coding genes for the differentially methylated miRNAs using messenger RNA expression data

Usage

find_miRNA_targets(
  EpiMixResults,
  geneExprData,
  database = "mirtarbase",
  raw.pvalue.threshold = 0.05,
  adjusted.pvalue.threshold = 0.2,
  cores = 1
)

Arguments

EpiMixResults	List of the result objects returned from the EpiMix function.
geneExprData	Matrix of the messenger RNA expression data with genes in rows and samples in columns.
database	character string indicating the database for retrieving miRNA targets. Default: "mirtarbase".
raw.pvalue.threshold	Numeric value indicating the threshold of the raw P value for selecting the miRNA targets based on gene expression. Default: 0.05.
adjusted.pvalue.threshold	Numeric value indicating the threshold of the adjusted P value for selecting the miRNA targets based on gene expression. Default: 0.2.
cores	Number of CPU cores to be used for computation. Default: 1.

Value

Matrix indicating the miRNA-target pairs, with fold changes of target gene expression and P values.

Examples

library(multiMiR)
library(miRBaseConverter)

data(mRNA.data)
data(Sample_EpiMixResults_miRNA)

miRNA_targets <- find_miRNA_targets(
 EpiMixResults = Sample_EpiMixResults_miRNA,
 geneExprData = mRNA.data
)

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.