FgseaList: FgseaList - wrapper around fast gene set enrichment analysis...

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

FgseaList - wrapper around fast gene set enrichment analysis with the fgsea R package https://bioconductor.org/packages/release/bioc/html/fgsea.html to implement on a list of ranks indexec by cell type.

Description

FgseaList - wrapper around fast gene set enrichment analysis with the fgsea R package https://bioconductor.org/packages/release/bioc/html/fgsea.html to implement on a list of ranks indexec by cell type.

Usage

FgseaList(..., rank.list.celltype, pathways, maxSize = 500, minSize = 9)

Arguments

rank.list.celltype	results returned by GetRankResultsRaw or GetRankResults
pathways	modules / gene sets as a named list each a single vector of unique gene IDS
maxSize	see fgsea package
minSize	see fgsea package

Value

results from fgsea package indexed by celltype

Examples

## Not run: 
t1hvl_rank = GetRankResultsRaw(limma.fit.object.list  = dreamfit,
coefficient.number = 1,
contrast.name = "contrastName")
register(SnowParam(4))
pparam = SnowParam(workers = 4, type = "SOCK", progressbar = TRUE)
gsealist = FgseaList(rank.list.celltype = t1hvl_rank, pathways = btm,  BPPARAM = pparam)

## End(Not run)
# usage:

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