GEX_GOterm | R Documentation |
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 )
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. |
Returns a list of data frames and plots containing the TopGO and the TopKEGG output containing the significant GO/KEGG terms and their visualizations.
## Not run: 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") ## End(Not run)
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