getDEGTopTable {singleCellTK} | R Documentation |
Users have to run runDEAnalysis()
first, any of the
wrapped functions of this generic function. Users can set further filters on
the result. A data.frame
object, with variables of Gene
,
Log2_FC
, Pvalue
, and FDR
, will be returned.
getDEGTopTable( inSCE, useResult, labelBy = NULL, onlyPos = FALSE, log2fcThreshold = 0.25, fdrThreshold = 0.05 )
inSCE |
SingleCellExperiment inherited object, with of the singleCellTK DEG method performed in advance. |
useResult |
character. A string specifying the |
labelBy |
A single character for a column of |
onlyPos |
logical. Whether to only fetch DEG with positive log2_FC
value. Default |
log2fcThreshold |
numeric. Only fetch DEGs with the absolute values of
log2FC larger than this value. Default |
fdrThreshold |
numeric. Only fetch DEGs with FDR value smaller than this
value. Default |
A data.frame
object of the top DEGs, with variables of
Gene
, Log2_FC
, Pvalue
, and FDR
.
data("sceBatches") sceBatches <- scaterlogNormCounts(sceBatches, "logcounts") sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'") sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha", groupName1 = "w.alpha", groupName2 = "w.beta", analysisName = "w.aVSb") getDEGTopTable(sce.w, "w.aVSb")