Get Marker Features from a marker summarized experiment

This function will identify Markers and return a List of Features or a GRangesList for each group of significant marker features.

getMarkers(
  seMarker = NULL,
  cutOff = "FDR <= 0.1 & Log2FC >= 0.5",
  n = NULL,
  returnGR = FALSE
)

Arguments

seMarker

A SummarizedExperiment object returned by getMarkerFeatures().

cutOff

A valid-syntax logical statement that defines which marker features from seMarker. cutoff can contain any of the assayNames from seMarker.

n

An integer that indicates the maximum number of features to return per group.

returnGR

A boolean indicating whether to return as a GRanges object. Only valid when seMarker is computed for a PeakMatrix.

Examples

#Get Test Project
proj <- getTestProject()

#Get Markers
seMarker <- getMarkerFeatures(
  ArchRProj = proj, 
  useMatrix = "PeakMatrix", 
  testMethod = "binomial", 
  binarize = TRUE
)

#Get Markers
getMarkers(seMarker)