filterData: Filter data from a 'GRN' object

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

Filter data from a GRN object

Description

Filter data from a GRN object

Usage

filterData(
  GRN,
  minNormalizedMean_peaks = 5,
  maxNormalizedMean_peaks = NULL,
  minNormalizedMeanRNA = 1,
  maxNormalizedMeanRNA = NULL,
  chrToKeep_peaks = c(paste0("chr", seq_len(22)), "chrX", "chrY"),
  minSize_peaks = NULL,
  maxSize_peaks = 10000,
  minCV_peaks = NULL,
  maxCV_peaks = NULL,
  minCV_genes = NULL,
  maxCV_genes = NULL,
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
minNormalizedMean_peaks	Numeric or NULL. Default 5. Minimum mean across all samples for a peak to be retained for the normalized counts table. Set to NULL for not applying the filter.
maxNormalizedMean_peaks	Numeric or NULL. Default NULL. Maximum mean across all samples for a peak to be retained for the normalized counts table. Set to NULL for not applying the filter.
minNormalizedMeanRNA	Numeric or NULL. Default 5. Minimum mean across all samples for a gene to be retained for the normalized counts table. Set to NULL for not applying the filter.
maxNormalizedMeanRNA	Numeric or NULL. Default NULL. Maximum mean across all samples for a gene to be retained for the normalized counts table. Set to NULL for not applying the filter.
chrToKeep_peaks	Character vector. Default c(paste0("chr", 1:22), "chrX", "chrY"). Vector of chromosomes that peaks are allowed to come from. This filter can be used to filter sex chromosomes from the peaks, for example.
minSize_peaks	Integer or NULL. Default NULL. Minimum peak size (width, end - start) for a peak to be retained. Set to NULL for not applying the filter.
maxSize_peaks	Integer or NULL. Default 10000. Maximum peak size (width, end - start) for a peak to be retained. Set to NULL for not applying the filter.
minCV_peaks	Numeric or NULL. Default NULL. Minimum CV (coefficient of variation, a unitless measure of variation) for a peak to be retained. Set to NULL for not applying the filter.
maxCV_peaks	Numeric or NULL. Default NULL. Maximum CV (coefficient of variation, a unitless measure of variation) for a peak to be retained. Set to NULL for not applying the filter.
minCV_genes	Numeric or NULL. Default NULL. Minimum CV (coefficient of variation, a unitless measure of variation) for a gene to be retained. Set to NULL for not applying the filter.
maxCV_genes	Numeric or NULL. Default NULL. Maximum CV (coefficient of variation, a unitless measure of variation) for a gene to be retained. Set to NULL for not applying the filter.
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 = filterData(GRN, forceRerun = FALSE)

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