Find differential expression genes for all clusters by comparing one cluster to the remaining clusters.

FindAllDEGs(
  spe,
  use_cluster = "clusters",
  features = NULL,
  logfc.threshold = 0.25,
  only.pos = FALSE,
  test.use = "wilcox",
  ...
)

Arguments

spe

A SpatialExperiment object with cluster labels for each cell/spot in colData.

use_cluster

a string, the name in colData denoting the cluster labels.

features

a string vector, specify the gene list to do differential gene expression analysis.

logfc.threshold

a real, the threshold of log fold change to determine which genes are returned.

only.pos

a logical value, whether only return the genes with positive log fold change.

test.use

a string, the test to use.

...

other arguments pass to FindAllMarkers.

Value

return a dataframe with the DEG analysis results.