runSeuratFindMarkers: runSeuratFindMarkers

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

runSeuratFindMarkers

Description

runSeuratFindMarkers

Usage

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.

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.