scDGE | R Documentation |
Differential gene expression analysis for each cluster Perform differential analysis (DE) between two groups for each clusters
scDGE(
object = object,
comparison = c("condA", "condB"),
group.by = NULL,
min.cells = 20,
min.pct = 0.1,
logFC = 0.25,
clusters = NULL
)
object |
Seurat object. |
comparison |
Vector of nominal variables from group.by. Eg., comparison=c('Normal', 'Tumor') |
group.by |
Regroup cells before performing DGE, default group.by='group' |
min.cells |
Minimum number of cells for DGE in any of the two groups, default min.cells=20 |
min.pct |
Genes expressed in any of the two groups with a minium cell fraction (min.pct) are reserved for DGE, default min.pct=0.1 |
logFC |
A positive value to set the cutoff of logFC, default logFC=0.25 |
clusters |
Vector of clusters to perform DGE, default clusters=NULL, which means all clusters will be evaluated |
DGE Table
FindMarkers
data("H3N2_small")
x <- scDGE(object = H3N2_small,
comparison = c("Infected", "Bystander"),
group.by = "group",
min.cells = 10,
logFC = 0.25,
clusters = NULL
)
head(x)
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