Calculate Differential Abundance with FET
diffAbundanceFET(inSCE, cluster, variable, control, case, analysisName)
inSCE | A |
---|---|
cluster | A single |
variable | A single |
control |
|
case |
|
analysisName | A single |
The original SingleCellExperiment
object with metadata(inSCE)
updated with a list
diffAbundanceFET
, containing a new data.frame
for the analysis
result, named by analysisName
. The data.frame
contains columns
for number and fraction of cells that belong to different cases, as well as
"Odds_Ratio", "PValue" and "FDR".
This function will calculate the cell counting and fraction by dividing all cells to groups specified by the arguments, together with statistical summary by performing Fisher Exact Tests (FET).
data("mouseBrainSubsetSCE", package = "singleCellTK") mouseBrainSubsetSCE <- diffAbundanceFET(inSCE = mouseBrainSubsetSCE, cluster = "tissue", variable = "level1class", case = "oligodendrocytes", control = "microglia", analysisName = "diffAbundFET")