cor_tf_target_gene {MethReg} | R Documentation

## Evaluate correlation of TF expression and target gene expression

### Description

This function evaluate the correlation of a TF 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_tf_target_gene(
      pair.tf.target,
      exp,
      tf.activity.es,
      cores = 1,
      verbose = FALSE
    )

### Arguments

`pair.tf.target` | A dataframe with the following columns: TF and target (target gene)
`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 tf.activity.es matrix
`tf.activity.es` | A matrix with normalized enrichment scores for each TF across all samples to be used in linear models instead of TF gene expression. See `get_tf_ES`.
`cores` | Number of CPU cores to be used. Default 1.
`verbose` | Show messages ?

### Value

A data frame with the following information: TF, target gene, correlation p-value and estimate between TF and target gene expression, FDR corrected p-values.

### Examples

    exp <- t(matrix(sort(c(runif(40))), ncol = 2))
    rownames(exp) <- c("ENSG00000232886","ENSG00000232889")
    colnames(exp) <- paste0("Samples",1:20)

    pair.tf.target <- data.frame(
       "TF" = "ENSG00000232889",
       "target" = "ENSG00000232886"
    )

    # Correlated TF and gene expression
    results.cor.pos <- cor_tf_target_gene(
       pair.tf.target = pair.tf.target,
       exp = exp,
    )
    # Correlated TF and gene expression
    results.cor.pos <- cor_tf_target_gene(
       pair.tf.target = pair.tf.target,
       exp = exp,
       tf.activity.es = exp
    )

[Package MethReg version 1.4.0 Index]