performGeneSetEnrichmentAnalysis: Perform gene set enrichment analysis with GSVA.

In romanhaa/cerebroPrepare: Export data for visualization in Cerebro.

Description

This function calculates enrichment scores, p- and q-value statistics for provided gene sets for samples and clusters 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, gene_sets_to_test,
  column_sample = "sample", column_cluster = "cluster",
  thresh_p_val = 0.05, thresh_q_val = 0.1, ...)

Arguments

object	Seurat object. log-counts for analysis must be stored in 'object@data' (Seurat object older than v3) or 'object@assays$RNA@data' (Seurat object v3 or newer).
column_sample	Column in [e-mail] that contains information about sample; defaults to 'sample'.
column_cluster	Column in [e-mail] that contains information about cluster; defaults to 'cluster'.
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().
gene_sets	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

Details

Perform gene set enrichment analysis with GSVA.

Examples

seurat <- performGeneSetEnrichmentAnalysis(
  object = seurat,
  gene_sets = 'path/to/gene_sets.gmt',
  column_sample = 'sample',
  column_cluster = 'cluster',
  thresh_p_val = 0.05,
  thresh_q_val = 0.1
)

romanhaa/cerebroPrepare documentation built on Oct. 17, 2019, 4:01 p.m.