addData: Add data 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 data to a GRN object

Description

Add data to a GRN object

Usage

addData(
  GRN,
  counts_peaks,
  normalization_peaks = "DESeq_sizeFactor",
  idColumn_peaks = "peakID",
  counts_rna,
  normalization_rna = "quantile",
  idColumn_RNA = "ENSEMBL",
  sampleMetadata = NULL,
  allowOverlappingPeaks = FALSE,
  forceRerun = FALSE
)

Arguments

GRN	Object of class GRN
counts_peaks	Data frame. No default. Counts for the peaks, with raw or normalized counts for each peak (rows) across all samples (columns). In addition to the count data, it must also contain one ID column with a particular format, see the argument idColumn_peaks below. Row names are ignored, column names must be set to the sample names and must match those from the RNA counts and the sample metadata table.
normalization_peaks	Character. Default DESeq_sizeFactor. Normalization procedure for peak data. Must be one of DESeq_sizeFactor, none, or quantile.
idColumn_peaks	Character. Default peakID. Name of the column in the counts_peaks data frame that contains peak IDs. The required format must be chr:start-end", with chr denoting the abbreviated chromosome name, and start and end the begin and end of the peak coordinates, respectively. End must be bigger than start. Examples for valid peak IDs are chr1:400-800 or chrX:20-25.
counts_rna	Data frame. No default. Counts for the RNA-seq data, with raw or normalized counts for each gene (rows) across all samples (columns). In addition to the count data, it must also contain one ID column with a particular format, see the argument idColumn_rna below. Row names are ignored, column names must be set to the sample names and must match those from the RNA counts and the sample metadata table.
normalization_rna	Character. Default quantile. Normalization procedure for peak data. Must be one of "DESeq_sizeFactor", "none", or "quantile"
idColumn_RNA	Character. Default ENSEMBL. Name of the column in the counts_rna data frame that contains Ensembl IDs.
sampleMetadata	Data frame. Default NULL. Optional, additional metadata for the samples, such as age, sex, gender etc. If provided, the @seealso [plotPCA_all()] function can then incorporate and plot it. Sample names must match with those from both peak and RNA-Seq data. The first column is expected to contain the sample IDs, the actual column name is irrelevant.
allowOverlappingPeaks	TRUE or FALSE. Default FALSE. Should overlapping peaks be allowed (then only a warning is issued when overlapping peaks are found) or (the default) should an error be raised?
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
# library(tidyverse)
# rna.df   = read_tsv("https://www.embl.de/download/zaugg/GRaNIE/rna.tsv.gz")
# peaks.df = read_tsv("https://www.embl.de/download/zaugg/GRaNIE/peaks.tsv.gz")
# meta.df  = read_tsv("https://www.embl.de/download/zaugg/GRaNIE/sampleMetadata.tsv.gz")
# GRN = loadExampleObject()
# We omit sampleMetadata = meta.df in the following line, becomes too long otherwise
# GRN = addData(GRN, counts_peaks = peaks.df, counts_rna = rna.df, forceRerun = FALSE)

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