findMarkerTopTable {singleCellTK} | R Documentation |
Fetch the table of top markers that pass the filtering
findMarkerTopTable( inSCE, log2fcThreshold = 1, fdrThreshold = 0.05, minClustExprPerc = 0.7, maxCtrlExprPerc = 0.4, minMeanExpr = 1, topN = 10 )
inSCE |
SingleCellExperiment inherited object. |
log2fcThreshold |
Only use DEGs with the absolute values of log2FC
larger than this value. Default |
fdrThreshold |
Only use DEGs with FDR value smaller than this value.
Default |
minClustExprPerc |
A numeric scalar. The minimum cutoff of the
percentage of cells in the cluster of interests that expressed the marker
gene. Default |
maxCtrlExprPerc |
A numeric scalar. The maximum cutoff of the
percentage of cells out of the cluster (control group) that expressed the
marker gene. Default |
minMeanExpr |
A numeric scalar. The minimum cutoff of the mean
expression value of the marker in the cluster of interests. Default |
topN |
An integer. Only to fetch this number of top markers for each
cluster in maximum, in terms of log2FC value. Use |
Users have to run findMarkerDiffExp()
prior to using this
function to extract a top marker table.
An organized data.frame
object, with the top marker gene
information.
data("mouseBrainSubsetSCE", package = "singleCellTK") mouseBrainSubsetSCE <- findMarkerDiffExp(mouseBrainSubsetSCE, useAssay = "logcounts", cluster = "level1class") findMarkerTopTable(mouseBrainSubsetSCE)