getDEGTopTable {singleCellTK}

R Documentation

Get Top Table of a DEG analysis

Description

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.

Usage

getDEGTopTable(
  inSCE,
  useResult,
  labelBy = NULL,
  onlyPos = FALSE,
  log2fcThreshold = 0.25,
  fdrThreshold = 0.05
)

Arguments

inSCE	SingleCellExperiment inherited object, with of the singleCellTK DEG method performed in advance.
useResult	character. A string specifying the analysisName used when running a differential expression analysis function.
labelBy	A single character for a column of rowData(inSCE) as where to search for the labeling text. Default NULL for the "rownames".
onlyPos	logical. Whether to only fetch DEG with positive log2_FC value. Default FALSE.
log2fcThreshold	numeric. Only fetch DEGs with the absolute values of log2FC larger than this value. Default 0.25.
fdrThreshold	numeric. Only fetch DEGs with FDR value smaller than this value. Default 0.05.

Value

A data.frame object of the top DEGs, with variables of Gene, Log2_FC, Pvalue, and FDR.

Examples

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")

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