FindGlobalMarkers {IRISFGM} | R Documentation |
FindGlobalMarkers
This function is for finding global marker FindGlobalMarkers is based on Seurat FindAllMarkers and the data from Tmp.seurat slots.
FindGlobalMarkers(object, ...) .findglobalMarkers( object = NULL, idents = NULL, logfc.threshold = 0.25, test.use = "wilcox", only.pos = TRUE, random.seed = 1, min.pct = 0.1 ) ## S4 method for signature 'IRISFGM' FindGlobalMarkers( object = NULL, idents = NULL, logfc.threshold = 0.25, test.use = "wilcox", only.pos = TRUE, random.seed = 1, min.pct = 0.1 )
object |
input IRIS-FGM object |
... |
other arguments passed to methods |
idents |
choose an idents for labelling cells |
logfc.threshold |
Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals. |
test.use |
same as |
only.pos |
keep postive result |
random.seed |
set seed for reproducibility |
min.pct |
only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1 |
Output is a differentially expressed gene list
data("example_object") markers <- FindGlobalMarkers( object = example_object, idents = "Seurat_r_0.8_k_20")