addConnections_TF_peak: Add TF-peak connections 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 TF-peak connections to a GRN object

Description

Add TF-peak connections to a GRN object

Usage

addConnections_TF_peak(
  GRN,
  plotDiagnosticPlots = TRUE,
  plotDetails = FALSE,
  outputFolder = NULL,
  corMethod = "pearson",
  connectionTypes = c("expression"),
  removeNegativeCorrelation = c(FALSE),
  maxFDRToStore = 0.3,
  useGCCorrection = FALSE,
  percBackground_size = 75,
  percBackground_resample = TRUE,
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
plotDiagnosticPlots	TRUE or FALSE. Default TRUE. Run and plot various diagnostic plots? If set to TRUE, PDF files will be produced and saved in the output directory (in a subfolder called plots).
plotDetails	TRUE or FALSE. Default FALSE. Print additional plots that may help for debugging and QC purposes? Note that these plots are currently less documented or not at all.
outputFolder	Character or NULL. Default NULL. If set to NULL, the default output folder as specified when initiating the object in link{initializeGRN} will be used. Otherwise, all output from this function will be put into the specified folder. We recommend specifying an absolute path.
corMethod	Character. pearson or spearman. Default pearson. Method for calculating the correlation coefficient. See cor for details.
connectionTypes	Character vector. Default expression. Vector of connection types to include for the TF-peak connections. If an additional connection type is specified here, it has to be available already within the object (EXPERIMENTAL). See the function addData_TFActivity for details.
removeNegativeCorrelation	Vector of TRUE or FALSE. Default FALSE. EXPERIMENTAL. Must be a logical vector of the same length as the parameter connectionType. Should negatively correlated TF-peak connections be removed for the specific connection type? For connection type expression, the default is FALSE, while for any TF Activity related connection type, we recommend setting this to TRUE.
maxFDRToStore	Numeric. Default 0.3. Maximum TF-peak FDR value to permanently store a particular TF-peak connection in the object? This parameter has a large influence on the overall memory size of the object, and we recommend not storing connections with a high FDR due to their sheer number.
useGCCorrection	TRUE or FALSE. Default FALSE. EXPERIMENTAL. Should a GC-matched background be used when calculating FDRs?
percBackground_size	Numeric (0 to 100). Default 75. EXPERIMENTAL. Description will follow. Only relevant if useGCCorrection is set to TRUE, ignored otherwise.
percBackground_resample	TRUE or FALSE. Default TRUE. EXPERIMENTAL. Should resampling be enabled for those GC bins for which not enough background peaks are available?. Only relevant if useGCCorrection is set to TRUE, ignored otherwise.
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 = addConnections_TF_peak(GRN, plotDiagnosticPlots = FALSE, forceRerun = FALSE)

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