run.diff.exp {iCellR} | R Documentation |
This function takes an object of class iCellR and performs differential expression (DE) analysis for clusters and conditions.
run.diff.exp( x = NULL, data.type = "main", de.by = "clusters", cond.1 = "array", cond.2 = "array", base.cond = 0 )
x |
An object of class iCellR. |
data.type |
Choose from "main" and "imputed", default = "main" |
de.by |
Choose from "clusters", "conditions", "clustBase.condComp" or "condBase.clustComp". |
cond.1 |
First condition to do DE analysis on. |
cond.2 |
Second condition to do DE analysis on. |
base.cond |
A base condition or cluster if de.by is either cond.clust or clust.cond |
An object of class iCellR
diff.res <- run.diff.exp(demo.obj, de.by = "clusters", cond.1 = c(1), cond.2 = c(2)) head(diff.res)