EnrichmentJaccard - using gsea list and LeadingEdgeIndexed result, compute pairwise jaccard index of leadingedge genes within celltypes. saves a heatmap of modules for each cell type in savpath if saveplot = TRUE. Returns a gsea result dataframe with all celltypes combined and module annotated with average within celltype jaccard index and leadingedge genes.

EnrichmentJaccard - using gsea list and LeadingEdgeIndexed result, compute pairwise jaccard index of leadingedge genes within celltypes. saves a heatmap of modules for each cell type in savpath if saveplot = TRUE. Returns a gsea result dataframe with all celltypes combined and module annotated with average within celltype jaccard index and leadingedge genes.

Usage

EnrichmentJaccard(
  ...,
  gsealist,
  indexedgenes,
  saveplot = FALSE,
  returnJaccardMtx = FALSE,
  figpath
)

Arguments

gsealist

results from FgseaList or RunFgseaOnRankList (recommend first lapply filter(padj < 0.05 e.g.) )

indexedgenes

results fro mLeadingEdgeIndexed

saveplot

if TRUE saves jaccard index heatmap to figpath

figpath

place to save figures, a file.path().

Value

curated dataframe of gsea results with average jaccard index.

Examples