diffgenes function

Compute Expression Differences between Clusters

This functions computes expression differences between clusters and ranks genes by z-score differences.

diffgenes(object, cl1, cl2, mincount = 1)

Arguments

• object: SCseq class object.
• cl1: A vector of valid cluster numbers (contained in the cpart slot of the SCseq object). Represents the first group of the comparison.
• cl2: A vector of valid cluster numbers (contained in the cpart slot of the SCseq object). Represents the second group of the comparison.
• mincount: Minimal normalized expression level of a gene to be included into the analysis. A gene needs to be expressed at this level in at least a single cell.

Returns

A list with four components: - z: a vector of z-scores in decreasing order with genes up-regulated in cl1 appearing at the top of the list.

• cl1: a data.frame with expression values for cells in cl1.

• cl2: a data.frame with expression values for cells in cl2.

• cl1n: a vector of cluster numbers for cells in cl1.

• cl2n: a vector of cluster numbers for cells in cl2.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
x <- diffgenes(sc,1,2)
head(x$z)
plotdiffgenes(x,names(x$z)[1])