Fetch the table of top markers that pass the filtering

Fetch the table of top markers that pass the filtering

getFindMarkerTopTable(
  inSCE,
  log2fcThreshold = 0,
  fdrThreshold = 0.05,
  minClustExprPerc = 0.5,
  maxCtrlExprPerc = 0.5,
  minMeanExpr = 0,
  topN = 1
)

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.

Value

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

Details

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

See also

runFindMarker, plotFindMarkerHeatmap

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runFindMarker(mouseBrainSubsetSCE,
                                     useAssay = "logcounts",
                                     cluster = "level1class")
#> Fri May  3 07:14:25 2024 ... Identifying markers for cluster 'microglia', using DE method 'wilcox'
#> Fri May  3 07:14:26 2024 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox'
#> Fri May  3 07:14:27 2024 ... Organizing findMarker result
getFindMarkerTopTable(mouseBrainSubsetSCE)
#>      Gene  Log2_FC       Pvalue          FDR      level1class clusterExprPerc
#> 1228 Apoe 4.439115 3.642815e-06 0.0001796628        microglia               1
#> 1002  Mal 5.361403 7.495067e-06 0.0002501837 oligodendrocytes               1
#>      ControlExprPerc clusterAveExpr
#> 1228       0.3333333       5.076598
#> 1002       0.4000000       6.370450