performGeneSetEnrichmentAnalysis: Perform gene set enrichment analysis with GSVA.

In romanhaa/cerebroApp: Interactive visualization of scRNA-seq data with Cerebro

Description

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).

Usage

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 [e-mail] 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
)

romanhaa/cerebroApp documentation built on Nov. 25, 2021, 5:29 p.m.