LeadEdgeTidySampleExprs - convert a PseudobulkList into a tidy dataframe for each sample across cell types of the leading edge genes from a gsea list

Usage

LeadEdgeTidySampleExprs(
  av.exprs.list,
  gsea.list,
  padj.filter,
  p.filter = NULL,
  NES.filter
)

Arguments

av.exprs.list: object returned by `PseudobulkList` summed or average counts
gsea.list: object returned by RunFgseaOnRankList
padj.filter: filter for adjusted p from GSEA
p.filter: filter for p from GSEA padj.filter must not be specified to use this option.
NES.filter: filter for normalized enrichment score from GSEA

Value

a list of tidy dataframes by celltype

Examples

if (FALSE) {
av = scglmmr::PseudobulkList(rawcounts = umi,
                             metadata = meta,
                             sample_col = "sample",
                             celltype_col = "celltype",
                             avg_or_sum = 'average')
le_expr = scglmmr::LeadEdgeTidySampleExprs(av.exprs.list = av,
                                           gsea.list = hlmk_ctm0,
                                           padj.filter = 0.1,
                                           NES.filter = -Inf)
}