logFC.RdThis function calculates the metric to be used for the gene set enrichment analysis. The most basic metric is the log fold-change in gene expression between a selected cluster and all other clusters, and is implemented here. Other possibile metrics could be used.
logFC(cluster.ids, expr.mat)
| cluster.ids | Named vector of the cluster identities assigned for each cell |
|---|---|
| expr.mat | Expression matrix with rows as genes and columns as cells |
Returns the log fold change in gene expression for each gene for cells in a cluster vs cells not in the cluster