Run GRaNIE Analysis — runGRaNIE • GRaNIEverse

This function runs the GRaNIE pipeline to generate gene regulatory network analyses from peak, RNA, and metadata files.

runGRaNIE(
  dir_output = "output_GRaNIE",
  datasetName = "undescribed",
  file_peaks,
  file_rna,
  file_metadata,
  TFBS_source = "custom",
  HOCOMOCO_version = "v12/H12INVIVO",
  TFBS_folder = NULL,
  TFBS_JASPAR_useSpecificTaxGroup = NULL,
  genomeAssembly = "hg38",
  normalization_peaks = "none",
  idColumn_peaks = "peakID",
  normalization_rna = "none",
  idColumn_RNA = "ENSEMBL",
  includeSexChr = FALSE,
  minCV = 0,
  minNormalizedMean_peaks = NULL,
  minNormalizedMean_RNA = NULL,
  minSizePeaks = 5,
  corMethod = "spearman",
  promoterRange = 250000,
  useGCCorrection = FALSE,
  GC_percBackground_size = 75,
  GC_percBackground_resample = TRUE,
  TF_peak.fdr.threshold = 0.2,
  peak_gene.fdr.threshold = 0.1,
  runTFClassification = FALSE,
  runNetworkAnalyses = FALSE,
  nCores = 4,
  forceRerun = TRUE
)

Arguments

dir_output: Character string specifying the directory where the output files will be saved. Default is `"output_GRaNIE"`.
datasetName: Character string specifying the name of the dataset. Default is `"undescribed"`. This is only used for populating the metadata in the GRaNIE object and has no functional consequence.
file_peaks: Character string specifying the path to the file containing peak data (i.e., one of the output files from `prepareSeuratData_GRaNIE`)
file_rna: Character string specifying the path to the file containing RNA data (i.e., one of the output files from `prepareSeuratData_GRaNIE`)
file_metadata: Character string specifying the path to the file containing metadata (i.e., one of the output files from `prepareSeuratData_GRaNIE`)
TFBS_source: Corresponds to the argument `source` from the method `addTFBS`. For more details, see the GRaNIE package description.
HOCOMOCO_version: Character string specifying the version of the HOCOMOCO database to use. Default is `"v12/H12INVIVO"`.
TFBS_folder: Corresponds to the argument `motifFolder` from the method `addTFBS`. For more details, see the GRaNIE package description.
TFBS_JASPAR_useSpecificTaxGroup: Corresponds to the argument `JASPAR_useSpecificTaxGroup` from the method `addTFBS`. For more details, see the GRaNIE package description.
genomeAssembly: Corresponds to the same-named argument from the method `initializeGRN`. For more details, see the GRaNIE package description.
normalization_peaks: Corresponds to the same-named argument from the method `addData`. For more details, see the GRaNIE package description.
idColumn_peaks: Corresponds to the same-named argument from the method `addData`. For more details, see the GRaNIE package description.
normalization_rna: Corresponds to the same-named argument from the method `addData`. For more details, see the GRaNIE package description.
idColumn_RNA: Corresponds to the same-named argument from the method `addData`. For more details, see the GRaNIE package description.
includeSexChr: Logical value indicating whether to include sex chromosomes in the analysis. Default is `FALSE`.
minCV: Corresponds to arguments `minCV_peaks` and `minCV_genes` from the method `filterData`. Currently, only one value for both modalities can be set. For more details, see the GRaNIE package description.
minNormalizedMean_peaks: Corresponds to the same-named argument from the method `filterData`. For more details, see the GRaNIE package description.
minNormalizedMean_RNA: Corresponds to the same-named argument from the method `filterData`. For more details, see the GRaNIE package description.
minSizePeaks: Corresponds to the same-named argument from the method `filterData`. For more details, see the GRaNIE package description.
corMethod: Character string specifying the correlation method to use (used in multiple functions within the GRaNIE workflow). Options are `"pearson"`, `"spearman"`, etc. Default is `"spearman"`.
promoterRange: Corresponds to the same-named argument from the method `addConnections_peak_geneInteger`. For more details, see the GRaNIE package description.
useGCCorrection: Corresponds to argument `useGCCorrection` from the method `addConnections_TF_peak`. For more details, see the GRaNIE package description.
GC_percBackground_size: Corresponds to argument `percBackground_size` from the method `addConnections_TF_peak`. For more details, see the GRaNIE package description.
GC_percBackground_resample: Corresponds to argument `percBackground_resample` from the method `addConnections_TF_peak`. For more details, see the GRaNIE package description.
TF_peak.fdr.threshold: Corresponds to the same-named argument from the method `filterGRNAndConnectGenes`. For more details, see the GRaNIE package description.
peak_gene.fdr.threshold: Corresponds to the same-named argument from the method `filterGRNAndConnectGenes`. For more details, see the GRaNIE package description.
runTFClassification: Logical value indicating whether to run transcription factor classification (function `AR_classification_wrapper`) in GRaNIE. Default is `FALSE`.
runNetworkAnalyses: Logical value indicating whether to run network analyses from GRaNIE (function `performAllNetworkAnalyses`). Default is `FALSE`.
nCores: Integer value specifying the number of cores to use for parallel processing that is used in multiple functions within the GRaNIE workflow. Default is `4`.
forceRerun: A logical value indicating whether to force rerun the function and re-generate the output even if the output files already exist on disk or in the object. Default is FALSE.

Value

The function processes the dataset and saves the results in the specified output directory.

Examples

if (FALSE) {
# Example usage:
runGRaNIE(
  dir_output = "results/",
  datasetName = "example_dataset",
  file_peaks = "data/peaks.tsv",
  file_rna = "data/rna.tsv",
  file_metadata = "data/metadata.tsv",
  TFBS_source = "JASPAR2024",
  nCores = 8
)
}