cor_dnam_target_gene {MethReg} | R Documentation

## Evaluate correlation of DNA methylation region and target gene expression

### Description

This function evaluate the correlation of the DNA methylation and target gene expression using spearman rank correlation test. Note that genes with RNA expression equal to 0 for all samples will not be evaluated.

### Usage

    cor_dnam_target_gene(
      pair.dnam.target,
      dnam,
      exp,
      filter.results = TRUE,
      min.cor.pval = 0.05,
      min.cor.estimate = 0,
      cores = 1
    )

### Arguments

`pair.dnam.target` | A dataframe with the following columns: regionID (DNA methylation) and target (target gene)
`dnam` | DNA methylation matrix or SummarizedExperiment object with regions/cpgs in rows and samples in columns are samples. Samples should be in the same order as gene expression matrix (exp).
`exp` | Gene expression matrix or SummarizedExperiment object (rows are genes, columns are samples) log2-normalized (log2(exp + 1)). Samples should be in the same order as the DNA methylation matrix.
`filter.results` | Filter results using min.cor.pval and min.cor.estimate thresholds
`min.cor.pval` | P-value threshold filter (default: 0.05)
`min.cor.estimate` | Correlation estimate threshold filter (default: not applied)
`cores` | Number of CPU cores to be used. Default 1.

### Value

A data frame with the following information: regionID, target gene, correlation pvalue and estimate between DNA methylation and target gene expression, FDR corrected p-values.

### Examples

    dnam <- t(matrix(sort(c(runif(20))), ncol = 1))
    rownames(dnam) <- c("chr3:203727581-203728580")
    colnames(dnam) <- paste0("Samples",1:20)
    exp <- dnam
    rownames(exp) <- c("ENSG00000232886")
    colnames(exp) <- paste0("Samples",1:20)

    pair.dnam.target <- data.frame(
       "regionID" =  c("chr3:203727581-203728580"),
       "target" = "ENSG00000232886"
    )

    # Correlated DNAm and gene expression, display only significant associations
    results.cor.pos <- cor_dnam_target_gene(
       pair.dnam.target = pair.dnam.target,
       dnam = dnam,
       exp = exp,
       filter.results = TRUE,
       min.cor.pval = 0.05,
       min.cor.estimate = 0.0
    )

[Package MethReg version 1.4.0 Index]