cor_dnam_target_gene: Evaluate correlation of DNA methylation region and target...

In TransBioInfoLab/MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

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
)

TransBioInfoLab/MethReg documentation built on July 28, 2023, 9:17 p.m.