Function reference • FigR

Peak-gene correlations

runGenePeakcorr(): Gene-Peak correlations used for calling domains of regulatory chromatin (DORCs)

dorcJPlot(): DORC J scatter plot

getDORCScores(): DORC scATAC-seq score summarization for single cells

TF-DORC associations

runFigRGRN(): Infer FigR TF-DORC associations

motifPeakZtest(): Peak-based TF motif enrichment Z-test

scATAC-scRNA scOptMatch cell pairing

pairCells(): Pair cells

plotPairs(): Plot ATAC-RNA scOptMatch pairs

Visualizing FigRGRN results

plotDrivers(): Plot FigR scatter profile

rankDrivers(): Rank TF drivers

plotfigRHeatmap(): Plot FigR heatmap

plotfigRNetwork(): Plot FigR Network

Miscellaneous helper functions

centerCounts(): Center single-cell ATAC-seq count data

smoothScoresNN(): Smooth single cell matrix using cell kNNs

plotMarker2D(): Plot marker scores on single cell scatter plots

splitAndFetch(): Split and fetch string subparts