Normalize cluster factor level order in a clustered gsList

Rebuilds every GSEA_snn_res.<res> metadata column so its factor levels are in numeric order (0, 1, 2, ...), starting at 0. Newer objects get this automatically inside clusterGeneSets(); use this to migrate objects clustered before that fix without re-clustering. Cluster assignments are unchanged – only the level order is corrected.

Usage

normalizeClusterLevels(geneSetsList)

Arguments

geneSetsList

A clustered 'gsList' object.

Value

The 'gsList' with normalized cluster factor level order.

Examples

gsListObject <- normalizeClusterLevels(exampleGsList)
levels(gsListObject@cluster$GSEA_snn_res.1.1)
#> [1] "0" "1" "2" "3" "4" "5"