addTFBS: Add TFBS to a 'GRN' object

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

Add TFBS to a GRN object

Description

Add TFBS to a GRN object

Usage

addTFBS(
  GRN,
  motifFolder,
  TFs = "all",
  nTFMax = NULL,
  filesTFBSPattern = "_TFBS",
  fileEnding = ".bed",
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
motifFolder	Character. No default. Path to the folder that contains the TFBS predictions. The files must be in BED format, 6 columns, one file per TF. See the other parameters for more details.
TFs	Character vector. Default all. Vector of TF names to include. The special keyword all can be used to include all TF found in the folder as specified by motifFolder. If all is specified anywhere, all TFs will be included. TF names must otherwise match the file names that are found in the folder, without the file suffix.
nTFMax	NULL or integer. Default NULL. Maximal number of TFs to import. Can be used for testing purposes, e.g., setting to 5 only imports 5 TFs even though the whole motifFolder has many more TFs defined.
filesTFBSPattern	Character. Default "_TFBS". Suffix for the file names in the TFBS folder that is not part of the TF name. Can be empty. For example, for the TF CTCF, if the file is called CTCF.all.TFBS.bed, set this parameter to ".all.TFBS".
fileEnding	Character. Default ".bed". File ending for the files from the motif folder.
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

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