run_gsea | R Documentation |
Use fgsea algorithm to compute normalized enrichment scores and pvalues for gene set ovelap
run_gsea(
expr_mat,
query_genes,
cluster_ids = NULL,
n_perm = 1000,
per_cell = FALSE,
scale = FALSE,
no_warnings = TRUE
)
expr_mat |
single-cell expression matrix or Seurat object |
query_genes |
A vector or named list of vectors of genesets of interest to compare via GSEA. If supplying a named list, then the gene set names will appear in the output. |
cluster_ids |
vector of cell cluster assignments, supplied as a
vector with order that
matches columns in |
n_perm |
Number of permutation for fgsea function. Defaults to 1000. |
per_cell |
if true run per cell, otherwise per cluster. |
scale |
convert expr_mat into zscores prior to running GSEA?, default = FALSE |
no_warnings |
suppress warnings from gsea ties |
dataframe of gsea scores (pval, NES), with clusters as rownames
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