runSeuratFindMarkers — runSeuratFindMarkers • singleCellTK

runSeuratFindMarkers

runSeuratFindMarkers(
  inSCE,
  cells1 = NULL,
  cells2 = NULL,
  group1 = NULL,
  group2 = NULL,
  allGroup = NULL,
  conserved = FALSE,
  test = "wilcox",
  onlyPos = FALSE,
  minPCT = 0.1,
  threshUse = 0.25,
  verbose = TRUE
)

Arguments

inSCE: Input SingleCellExperiment object.
cells1: A list of sample names included in group1.
cells2: A list of sample names included in group2.
group1: Name of group1.
group2: Name of group2.
allGroup: Name of all groups.
conserved: Logical value indicating if markers conserved between two groups should be identified. Default is FALSE.
test: Test to use for DE. Default "wilcox".
onlyPos: Logical value indicating if only positive markers should be returned.
minPCT: Numeric value indicating the minimum fraction of min.pct cells in which genes are detected. Default is 0.1.
threshUse: Numeric value indicating the logFC threshold value on which on average, at least X-fold difference (log-scale) between the two groups of cells exists. Default is 0.25.
verbose: Logical value indicating if informative messages should be displayed. Default is TRUE.

Value

A SingleCellExperiment object that contains marker genes populated in a data.frame stored inside metadata slot.