The data frame is the direct output of marker detection DEG test applied on
example dataset which can be loaded with data("pbmc"). The DEG test
was done with:
defaultCluster(pbmc) <- pbmcPlot$leiden_cluster
deg.marker <- runMarkerDEG(
pbmc,
minCellPerRep = 5
)The result is for the marker detection test for 8 clusters in the dataset by comparing each cluster against all other clusters.
Format
data.frame object of 1992 rows with columns:
feature: gene names, 249 unique genes repeated 8 times for the tests done for 8 clusters.
group: cluster names, 8 unique cluster names, dividing the tests.
logFC: log fold change of the gene expression between the cluster of interest against all other clusters.
pval: p-value of the DEG test.
padj: adjusted p-value of the DEG test.
pct_in: percentage of cells in the cluster of interest expressing the gene.
pct_out: percentage of cells in all other clusters expressing the gene.