getFindMarkerTopTable: Fetch the table of top markers that pass the filtering

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

Fetch the table of top markers that pass the filtering

Description

Fetch the table of top markers that pass the filtering

Usage

getFindMarkerTopTable(
  inSCE,
  log2fcThreshold = 1,
  fdrThreshold = 0.05,
  minClustExprPerc = 0.7,
  maxCtrlExprPerc = 0.4,
  minMeanExpr = 1,
  topN = 10
)

findMarkerTopTable(
  inSCE,
  log2fcThreshold = 1,
  fdrThreshold = 0.05,
  minClustExprPerc = 0.7,
  maxCtrlExprPerc = 0.4,
  minMeanExpr = 1,
  topN = 10
)

Arguments

inSCE	SingleCellExperiment inherited object.
log2fcThreshold	Only use DEGs with the absolute values of log2FC larger than this value. Default 1
fdrThreshold	Only use DEGs with FDR value smaller than this value. Default 0.05
minClustExprPerc	A numeric scalar. The minimum cutoff of the percentage of cells in the cluster of interests that expressed the marker gene. Default 0.7.
maxCtrlExprPerc	A numeric scalar. The maximum cutoff of the percentage of cells out of the cluster (control group) that expressed the marker gene. Default 0.4.
minMeanExpr	A numeric scalar. The minimum cutoff of the mean expression value of the marker in the cluster of interests. Default 1.
topN	An integer. Only to fetch this number of top markers for each cluster in maximum, in terms of log2FC value. Use NULL to cancel the top N subscription. Default 10.

Details

Users have to run runFindMarker prior to using this function to extract a top marker table.

Value

An organized data.frame object, with the top marker gene information.

See Also

runFindMarker, plotFindMarkerHeatmap

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runFindMarker(mouseBrainSubsetSCE,
                                     useAssay = "logcounts",
                                     cluster = "level1class")
getFindMarkerTopTable(mouseBrainSubsetSCE)

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.