Description Usage Arguments Value
This function takes an object of class iCellR and performs differential expression (DE) analysis for clusters and conditions.
1 2 3 4 5 6 7 8 9 10 | run.diff.exp(
x = NULL,
data.type = "main",
pval.test = "t.test",
p.adjust.method = "hochberg",
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" |
pval.test |
Choose from "t.test", "wilcox.test", default = "t.test". |
p.adjust.method |
Correction method. Choose from "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none", default = "hochberg". |
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
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