getDORCScores: DORC scATAC-seq score summarization for single cells

In buenrostrolab/FigR: Functional Inference of Gene Regulation (FigR) using paired single cell ATAC-seq and RNA-seq data

DORC scATAC-seq score summarization for single cells

Description

Function to compute single cell DORC scores for each gene identified as a DORC (see runGenePeakcorr for determining DORCs through peak-gene correlations)

Usage

getDORCScores(
  ATAC.se,
  dorcTab,
  normalizeATACmat = TRUE,
  geneList = NULL,
  nCores = 4
)

Arguments

ATAC.se	SummarizedExperiment object of the scATAC-seq reads in peak counts.
dorcTab	data.frame object containing significant peak-gene pairs using which DORC scores will be computed. Must be a filtered set returned from runGenePeakcorr. IMPORTANT: Make sure the exact same scATAC SE (peak set) was used when determining DORCs that is used here to get corresponding DORC peak counts
normalizeATACmat	boolean indicating whether or not to normalize the counts present in the ATAC.se object prior to summing peak counts per gene. Default is TRUE (i.e. assumes peak counts are raw).
geneList	character vector specifying a subset of genes to compute scores for. Useful if you already have a set list of DORCs and you only want to compute scores for those genes/peaks.
nCores	numeric indicating the number of cores to use if parallelizing tasks

Value

a Matrix object of scores pertaining to the sum of normalized scATAC peak counts per gene, as determined for significant gene-peak pairs when calling DORCs

Author(s)

Vinay Kartha

buenrostrolab/FigR documentation built on Feb. 10, 2023, 11:26 a.m.