miRNACorrel: Get microRNA-target Interactions and compute correlations

In margenomics/microTargets: Retrieve microRNA-target Interactions and Compute Correlations

Get microRNA-target Interactions and compute correlations

Description

Main function to retrieve interactions between a set of miRNAs and a set of genes and computes correlations given expression data. The function calls miRNAGenes.updated function which uses TargetScan, miRDB and mirTarBase.

Usage

miRNACorrel(
  DE.miRNA,
  DE.target,
  counts.miRNA,
  counts.mRNA,
  cols.s = NULL,
  resultsDir = getwd(),
  name = "Summary"
)

Arguments

DE.miRNA	Character string or character vector of miRNA(s)
DE.target	Character string or character vector of mRNA(s)
counts.miRNA	Table of miRNA counts. First column contains miRNA ID's (miRBase v21)
counts.mRNA	Table of mRNA counts with sample columns in teh same order as counts.miRNA. First column contains Symbol IDs
cols.s	Vector with colors corresponding to the conditions of each sample
resultsDir	Output directory (default working dir)
name	Name of the output files (default "Summary")
path	Character string with the path to where the database files are stored

Value

The function returns a dataframe with all miRNAs and the number of targets identified and the number of targets significantly negatively correlated for each miRNA. It also generates: a) excel file with one sheet per miRNA, in which the correlations results for each target are shown (Rho and p.value of the spearman correlation); b) pdf with correlation plots for each miRNA-target pair

Author(s)

Julia Perera Bel <[e-mail]>

margenomics/microTargets documentation built on Aug. 22, 2023, 2:26 a.m.