GEX_GSEA | R Documentation |
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.
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, verbose )
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 == T. 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. |
verbose |
Print run parameters and status to console |
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.
## Not run: df <- GEX_cluster_genes(gex_combined[[1]]) #Using gmt file to perform gsea 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) View(gex_gsea[[1]]) #Directly downloading gene set collection from MSigDB to perform gsea output <- GEX_GSEA(GEX.cluster.genes.output = df[[1]], MT.Rb.filter = TRUE , path.to.pathways = c("Mus musculus", "C7")) #Using your own gene list to perform gsea output <- GEX_GSEA(GEX.cluster.genes.output = df[[1]], MT.Rb.filter = TRUE , my.own.geneset = my_geneset) ## End(Not run)
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