Find miRNAs target using mRNA/miRNA expression

Source: R/targets.R

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.

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)

#> Number of mirnas 20
#> Number of genes 20
#> Factors genescontrolday1day2day3day7day14
#> Factors mirnascontrolday1day2day3day7day14
#> Order genescontrolcontrolcontrolday1day1day1day2day2day2day3day3day3day7day7day7day14day14day14
#> Order mirnascontrolcontrolcontrolday1day1day1day2day2day2day3day3day3day7day7day7day14day14day14
#> Calculating correlation matrix
#> Dimmension of cor matrix: 20 20