LeadEdgeTidySampleExprs: LeadEdgeTidySampleExprs - convert a PseudobulkList into a...

In MattPM/scglmmr: Sample-level Single-cell Generalized Linear Multilevel Models in R

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

Description

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

## Not run: 
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)

## End(Not run)

MattPM/scglmmr documentation built on April 26, 2024, 12:55 a.m.