cor_tf_target_gene: Evaluate correlation of TF expression and target gene...

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

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
)

MethReg documentation built on Nov. 8, 2020, 8:01 p.m.