test, forwarded to Seurat::FindAllMarkers()/Seurat::FindMarkers():
"wilcox" (Wilcoxon rank sum, the default), "roc" (classification power
from 0 = random to 1 = perfect), "bimod" (McDavid et al. 2013), "tobit"
(Trapnell et al. 2014), or "MAST" (Finak et al. 2015).
Usage
calculate_cluster_markers(x, label, test, pairwise = FALSE)
Arguments
- x
Seurat object with an identity set.
- label
Suffix for the output filenames.
- test
Statistical test - see above.
- pairwise
Compare clusters pairwise instead of each cluster against all
others - see above.
Value
x, invisibly. Called for its file and plot output.
Details
pairwise = TRUE compares each cluster against each other cluster
individually (rather than each cluster against all others combined), keeping
only genes significant in every comparison - local and global markers both,
at the cost of being much slower for many clusters.