findTargets: Find miRNAs target using mRNA/miRNA expression

In isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Description

This function creates a matrix with rows (genes) and columns (mirnas) with values indicating if miRNA-gene pair is target according putative targets and negative correlation of the expression of both molecules.

Usage

findTargets(mirna_rse, gene_rse, target, summarize = "group", min_cor = -0.6)

Arguments

mirna_rse	SummarizedExperiment with miRNA information. See details.
gene_rse	SummarizedExperiment with gene information. See details.
target	Data.frame with two columns: gene and miRNA.
summarize	Character column name in colData(rse) to use to group samples and compare betweem miRNA/gene expression.
min_cor	Numeric cutoff for correlation value that will be use to consider a miRNA-gene pair as valid.

Value

mirna-gene matrix

Examples

data(isoExample)
mirna_ma <- data.frame(gene = names(gene_ex_rse)[1:20],
                       mir = names(mirna_ex_rse))
corMat <- findTargets(mirna_ex_rse, gene_ex_rse, mirna_ma)

isomiRs documentation built on Jan. 31, 2021, 2 a.m.