diff.exp: Differential expression (DE) analysis

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Differential expression (DE) analysis

Description

This function takes an object of class scSeqR and performs differential expression (DE) analysis for clusters and conditions.

Usage

diff.exp(x = NULL, de.by = "clusters", cond.1 = "array",
  cond.2 = "array", base.cond = 0)

Arguments

x	An object of class scSeqR.
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

Value

An object of class scSeqR

Examples

## Not run: 
diff.res <- diff.exp(my.obj, de.by = "clusters", cond.1 = c(1,4), cond.2 = c(2))
diff.res <- diff.exp(my.obj, de.by = "conditions", cond.1 = c("WT"), cond.2 = c("KO"))
diff.res <- diff.exp(my.obj, de.by = "clustBase.condComp", cond.1 = c("WT"), cond.2 = c("KO"), base.cond = 1)
diff.res <- diff.exp(my.obj, de.by = "condBase.clustComp", cond.1 = c(1), cond.2 = c(2), base.cond = "WT")

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.