GEX GO-Term analysis and plotting — GEX

Runs a GO term analysis on a submitted list of genes. Works with the output of GEX_topN_DE_genes_per_cluster or a custom list of genes to obtain GOterms.

GEX_GOterm(
  GEX.cluster.genes.output,
  topNgenes,
  ontology,
  species,
  up.or.down,
  MT.Rb.filter,
  kegg,
  go.plots,
  top.N.go.terms.plots,
  kegg.plots,
  top.N.kegg.terms.plots,
  use.intput.list.as.title
)

Arguments

GEX.cluster.genes.output: Either output of Platypus::GEX_cluster_genes or custom character vector containing gene symbols. A custom gene list will not be further filtered or ordered.
topNgenes: How many of the most significant up or down regulated genes should be considered for GO term analysis. All genes will be used if left empty.
ontology: Ontology used for the GO terms. "MF", "BP" or "CC" possible. Default: "BP"
species: The species the genes belong to. Default: "Mm" (requires the package "org.Mm.eg.db"). Set to "Hs" for Human (requires the package "org.Hs.eg.db")
up.or.down: Whether up or downregulated genes should be used for GO term analysis if GEX_cluster_genes output is used. Default: "up"
MT.Rb.filter: logical, if mitochondrial and ribosomal genes should be filtered out.
kegg: logical, if KEGG pathway analysis should be conducted. Requires internet connection. Default: False.
go.plots: logical, if top GO-terms should be visualized. Default: False. If True, for each cluster the top N (top.N.GO.terms.plots) Go-terms for each cluster will be plotted to the working directory and saved as a list element. Plots are made both based on padj and ratio.
top.N.go.terms.plots: The number of most significant GO-terms to be incluted in the go.plots. Default: 10.
kegg.plots: logical, if top KEGG-terms should be visualized. Default: False. If True, for each cluster the top N (top.N.kegg.terms.plots) KEGG-terms for each cluster will be plotted to the working directory and saved as a list element. Plots are made both based on padj and ratio.
top.N.kegg.terms.plots: The number of most significant KEGG-terms to be incluted in the kegg.plots. Default: 10.

Value

Returns a list of data frames and plots containing the TopGO and the TopKEGG output containing the significant GO/KEGG terms and their visualizations.

Examples

if (FALSE) {

GEX_GOterm(DE_genes_cluster,MT.Rb.filter = TRUE, ontology = "MF")
GEX_GOterm(rownames(DE_genes_cluster[[1]]),MT.Rb.filter = TRUE, species= "Mm",
ontology = "BP", go.plots = TRUE)

#Install the needed database with
#if (!requireNamespace("BiocManager", quietly = TRUE))
#install.packages("BiocManager")
#BiocManager::install("org.Mm.eg.db")
#BiocManager::install("org.Hs.eg.db")
}