GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

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The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.

Author
Kevin Rue-Albrecht [aut, cre], Tharvesh M.L. Ali [ctb], Paul A. McGettigan [ctb], Belinda Hernandez [ctb], David A. Magee [ctb], Nicolas C. Nalpas [ctb], Andrew Parnell [ctb], Stephen V. Gordon [ths], David E. MacHugh [ths]
Date of publication
None
Maintainer
Kevin Rue-Albrecht <kevinrue67@gmail.com>
License
GPL (>= 3)
Version
1.8.1
URLs

View on Bioconductor

Man pages

AlvMac
Sample data from a RNAseq experiment.
AlvMac_allgenes
Example of custom gene feature annotations.
AlvMac_allGO
Example of custom gene ontology annotations.
AlvMac_GOgenes
Example of custom mapping between gene ontology identifiers...
AlvMac_results
Sample output from the 'GO_analyse()' function on an RNAseq...
AlvMac_results.pVal
Sample output from the 'pValue_GO()' function on an RNAseq...
cluster_GO
Generates a hierarchical clustering of the samples
expression_plot
Plots the expression profile of a gene by levels of a factor
expression_plot_symbol
Plots the expression profile of a gene by levels of a factor
expression_profiles
Plots the individual expression profile of a gene in samples...
expression_profiles_symbol
Plots the individual expression profile of a gene in samples...
GO_analyse
Identifies gene ontologies clustering samples according to...
GOexpress-package
Visualise microarray and RNAseq data with gene ontology...
heatmap_GO
Generates a heatmap and hierarchical clustering of the...
hist_scores
Plots the distribution of scores following an GOexpress...
list_genes
Returns the genes associated with a Gene Ontology
microarray2dataset
Table mapping probeset identifier prefixes to datasets in the...
overlap_GO
Shared genes between a list of GO terms.
plot_design
Plot Univariate Effects for genes associated with a Gene...
prefix2dataset
Table mapping Ensembl gene identifier prefixes to BioMart...
pValue_GO
Compute p-values for ontologies by randomising gene labels.
quantiles_scores
Returns the quantiles of scores following an GOexpress...
rerank
Reorder the result variable by alternative metrics.
subEset
Subset an ExpressionSet to values of phenotypic data columns.
subset_scores
Returns a filtered list from GO_analyse results.
table_genes
Returns a table listing the genes associated with a given...

Files in this package

GOexpress/DESCRIPTION
GOexpress/NAMESPACE
GOexpress/NEWS
GOexpress/R
GOexpress/R/analysis.R
GOexpress/R/post_analysis.R
GOexpress/R/toolkit.R
GOexpress/README.md
GOexpress/build
GOexpress/build/vignette.rds
GOexpress/data
GOexpress/data/AlvMac.RData
GOexpress/data/AlvMac_GOgenes.RData
GOexpress/data/AlvMac_allGO.RData
GOexpress/data/AlvMac_allgenes.RData
GOexpress/data/AlvMac_results.RData
GOexpress/data/AlvMac_results.pVal.RData
GOexpress/data/datalist
GOexpress/data/microarray2dataset.RData
GOexpress/data/prefix2dataset.RData
GOexpress/inst
GOexpress/inst/doc
GOexpress/inst/doc/GOexpress-UsersGuide.R
GOexpress/inst/doc/GOexpress-UsersGuide.Rnw
GOexpress/inst/doc/GOexpress-UsersGuide.pdf
GOexpress/man
GOexpress/man/AlvMac.Rd
GOexpress/man/AlvMac_GOgenes.Rd
GOexpress/man/AlvMac_allGO.Rd
GOexpress/man/AlvMac_allgenes.Rd
GOexpress/man/AlvMac_results.Rd
GOexpress/man/AlvMac_results.pVal.Rd
GOexpress/man/GO_analyse.Rd
GOexpress/man/GOexpress-package.Rd
GOexpress/man/cluster_GO.Rd
GOexpress/man/expression_plot.Rd
GOexpress/man/expression_plot_symbol.Rd
GOexpress/man/expression_profiles.Rd
GOexpress/man/expression_profiles_symbol.Rd
GOexpress/man/heatmap_GO.Rd
GOexpress/man/hist_scores.Rd
GOexpress/man/list_genes.Rd
GOexpress/man/microarray2dataset.Rd
GOexpress/man/overlap_GO.Rd
GOexpress/man/pValue_GO.Rd
GOexpress/man/plot_design.Rd
GOexpress/man/prefix2dataset.Rd
GOexpress/man/quantiles_scores.Rd
GOexpress/man/rerank.Rd
GOexpress/man/subEset.Rd
GOexpress/man/subset_scores.Rd
GOexpress/man/table_genes.Rd
GOexpress/vignettes
GOexpress/vignettes/GOexpress-UsersGuide.Rnw
GOexpress/vignettes/images
GOexpress/vignettes/images/shiny_screenshot.png