add_TF_gene_correlation: Add TF-gene correlations to a 'GRN' object. The information...

In chrarnold/GRaNIE: GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

Add TF-gene correlations to a GRN object. The information is currently stored in GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted.

Description

Add TF-gene correlations to a GRN object. The information is currently stored in GRN@connections$TF_genes.filtered. Note that raw p-values are not adjusted.

Usage

add_TF_gene_correlation(
  GRN,
  corMethod = "pearson",
  addRobustRegression = FALSE,
  nCores = 1,
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
corMethod	Character. pearson or spearman. Default pearson. Method for calculating the correlation coefficient. See cor for details.
addRobustRegression	TRUE or FALSE. EXPERIMENTAL. Default FALSE. Use a robust regression in addition to a non-robust one? Significantly increases overall running time.
nCores	Integer >0. Default 1. Number of cores to use.
forceRerun	TRUE or FALSE. Default FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.

Value

The same GRN object, with added data from this function.

Examples

# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
GRN = add_TF_gene_correlation(GRN, forceRerun = FALSE)

chrarnold/GRaNIE documentation built on April 28, 2022, 2:18 a.m.