# Visualise microarray and RNAseq data using gene ontology annotations

## Documentation for package ‘GOexpress’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

GOexpress-package | Visualise microarray and RNAseq data with gene ontology annotations.
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 and gene features.
AlvMac_results | Sample output from the 'GO_analyse()' function on an RNAseq experiment.
AlvMac_results.pVal | Sample output from the 'pValue_GO()' function on an RNAseq experiment.
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 series
expression_profiles_symbol | Plots the individual expression profile of a gene in samples series
GOexpress | Visualise microarray and RNAseq data with gene ontology annotations.
GO_analyse | Identifies gene ontologies clustering samples according to predefined factor.
heatmap_GO | Generates a heatmap and hierarchical clustering of the samples and the genes
hist_scores | Plots the distribution of scores following an GOexpress analysis.
list_genes | Returns the genes associated with a Gene Ontology
microarray2dataset | Table mapping probeset identifier prefixes to datasets in the Ensembl BioMart.
plot_design | Plot Univariate Effects for genes associated with a Gene Ontology
prefix2dataset | Table mapping Ensembl gene identifier prefixes to BioMart datasets.
pValue_GO | Compute p-values for ontologies by randomising gene labels.
quantiles_scores | Returns the quantiles of scores following an GOexpress analysis.
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 Gene Ontology