GEX_GSEA: GEX Gene Set Enrichment Analysis and plotting

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

GEX Gene Set Enrichment Analysis and plotting

Description

Conducts a Gene Set Enrichment Analysis (GSEA) on a set of genes submitted in a data frame with a metric each. Works with the output of GEX_genes_cluster or a custom data frame containing the gene symbols either in a column "symbols" or as rownames and a metric for each gene. The name of the column containing the metric has to be declared via the input metric.colname.

Usage

GEX_GSEA(
  GEX.cluster.genes.output,
  MT.Rb.filter,
  filter,
  path.to.pathways,
  metric.colname,
  pval.adj.cutoff,
  Enrichment.Plots,
  my.own.geneset,
  eps,
  platypus.version
)

Arguments

GEX.cluster.genes.output	Data frame containing the list of gene symbols and a metric. Function works directly with GEX_cluster_genes output.
MT.Rb.filter	Logical, should Mitotic and Ribosomal genes be filtered out of the geneset. True by default.
filter	Character vector containing the identifying symbol sequence for the genes which should be filtered out, if MT.Rb.filter == TRUE. By default set to c("MT-", "RPL", "RPS").
path.to.pathways	Either a path to gmt file containing the gene sets (can be downloaded from MSigDB) or vector where first element specifies species and second element specifies the MSigDB collection abbreviation. E.g.: c("Homo sapiens", "H"). Mouse C7 (immunologic signature) gene set will be used by default.
metric.colname	Name of column which contains the metric used for the ranking of the submitted genelist. "avg_logFC" is used by default.
pval.adj.cutoff	Only genes with a more significant adjusted pvalue are considered. Default: 0.001
Enrichment.Plots	List of Gene-set names which should be plotted as Enrichment plots in addition to the top 10 Up and Downregulated Genesets.
my.own.geneset	A list, where each element contains a gene list and is named with the corresponding pathway name. Default is set to FALSE, so that gene sets from MSigDB are used. Should not contain ".gmt" in name.
eps	Numeric, specifying boundary for calculating the p value in the GSEA.
platypus.version	Function works with V2 and V3, no need to set this parameter.

Value

Returns a list containing a tibble with the gene sets and their enrichment scores and Enrichment plots. List element [[1]]: Dataframe with Genesets and statistics. [[2]]: Enrichment plots of top10 Up regulated genesets. [[3]]: Enrichment plots of top10 Down regulated genesets. [[4]]: Enrichment plots of submited gene-sets in parameter Enrichment.Plot.

Examples

try({
df <- GEX_cluster_genes(Platypus::small_vgm[[2]])

output <- GEX_GSEA(GEX.cluster.genes.output =  df[[1]], MT.Rb.filter = TRUE
, path.to.pathways = "./c5.go.bp.v7.2.symbols.gmt")
cowplot::plot_grid(plotlist=output[[2]], ncol=2)

output <- GEX_GSEA(GEX.cluster.genes.output =  df[[1]], MT.Rb.filter = TRUE
, path.to.pathways = c("Mus musculus", "C7"))

output <- GEX_GSEA(GEX.cluster.genes.output =  df[[1]], MT.Rb.filter = TRUE
, my.own.geneset = my_geneset)
})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.