Perform gene set enrichment analysis with GSVA.

This function calculates enrichment scores, p- and q-value statistics for provided gene sets for specified groups of cells in given Seurat object using gene set variation analysis (GSVA). Calculation of p- and q-values for gene sets is performed as done in "Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data", Diaz-Mejia et al., F1000Research (2019).

performGeneSetEnrichmentAnalysis(
  object,
  assay = "RNA",
  GMT_file,
  groups = NULL,
  name = "cerebro_GSVA",
  thresh_p_val = 0.05,
  thresh_q_val = 0.1,
  ...
)

Arguments

object	Seurat object.
assay	Assay to pull counts from; defaults to 'RNA'. Only relevant in Seurat v3.0 or higher since the concept of assays wasn't implemented before.
GMT_file	Path to GMT file containing the gene sets to be tested. The Broad Institute provides many gene sets which can be downloaded: http://software.broadinstitute.org/gsea/msigdb/index.jsp
groups	Grouping variables (columns) in object@meta.data for which gene set enrichment analysis should be performed
name	Name of list that should be used to store the results in object@misc$enriched_pathways$<name>; defaults to 'cerebro_GSVA'.
thresh_p_val	Threshold for p-value, defaults to 0.05.
thresh_q_val	Threshold for q-value, defaults to 0.1.
...	Further parameters can be passed to control GSVA::gsva().

Value

Seurat object with GSVA results for the specified grouping variables stored in object@misc$enriched_pathways$<name>

Examples

pbmc <- readRDS(system.file("extdata/v1.3/pbmc_seurat.rds",
  package = "cerebroApp"))
example_gene_set <- system.file("extdata/example_gene_set.gmt",
  package = "cerebroApp")
pbmc <- performGeneSetEnrichmentAnalysis(
  object = pbmc,
  GMT_file = example_gene_set,
  groups = c('sample','seurat_clusters'),
  thresh_p_val = 0.05,
  thresh_q_val = 0.1
)
#> [17:53:55] Loading gene sets...
#> [17:53:55] Loaded 2 gene sets from GMT file.
#> [17:53:55] Extracting transcript counts from `data` slot of `RNA` assay...
#> [17:53:55] Performing analysis for 2 subgroups of group `sample`...
#> Estimating GSVA scores for 2 gene sets.
#> Estimating ECDFs with Gaussian kernels
#> 
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#> 
#> [17:53:55] 0 gene sets passed the thresholds across all subgroups of group `sample`.
#> [17:53:55] Performing analysis for 3 subgroups of group `seurat_clusters`...
#> Estimating GSVA scores for 2 gene sets.
#> Estimating ECDFs with Gaussian kernels
#> 
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#> 
#> [17:53:55] 0 gene sets passed the thresholds across all subgroups of group `seurat_clusters`.