pegasus.fgsea¶
- pegasus.fgsea(data, log2fc_key, pathways, de_key='de_res', minSize=15, maxSize=500, nproc=0, seed=0, fgsea_key='fgsea_out')[source]¶
Perform Gene Set Enrichment Analysis using fGSEA. This function calls R package fGSEA, requiring fGSEA in R installed.
- Parameters
data (Union[
MultimodalData
,UnimodalData
]) – Single-cell or pseudo-bulk data.log2fc_key (
str
) – Key in pre-computed DE results representing log2 fold change.pathways (
str
) – Either a string or a path to the gene set file in GMT format. If string, choosing from “hallmark” and “canonical_pathways” (MSigDB H and C2/CP).de_key (
str
, optional, default:"de_res"
) – Key name of DE analysis results stored. data.varm[de_key] should contain a record array of DE results.minSize (
int
, optional, default:15
) – Minimal size of a gene set to consider.maxSize (
int
, optional, default:500
) – Maximal size of a gene set to consider.nproc (
int
, optional, default:0
) – Numbr of processes for parallel computation. If nproc > 0, set BPPARAM.seed (
int
, optional, default:0
) – Random seed to make sure fGSEA results are reproducible.fgsea_key (
str
, optional, default:"fgsea_out"
) – Key to use to store fGSEA results as a data frame.
- Return type
None
- Returns
None
Update
data.uns
–data.uns[fgsea_key]
: fGSEA outputs sorted by padj.
Examples
>>> pg.fgsea(data, '3:log2FC', hallmark', fgsea_key='fgsea_res')