Visualise microarray and RNAseq data using gene ontology annotations


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Documentation for package ‘GOexpress’ version 1.6.1

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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.
overlap_GO Shared genes between a list of GO terms.
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