Word cloud summaries of GO enrichment analysis


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Documentation for package ‘GOsummaries’ version 1.1

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GOsummaries-package Word cloud summaries of GO enrichment analysis
add_expression.gosummaries Add expression data to gosummaries object
add_to_slot.gosummaries Functions for working with gosummaries object
customize Customization function for panel
GOsummaries Word cloud summaries of GO enrichment analysis
gosummaries Constructor for gosummaries object
gosummaries.default Constructor for gosummaries object
gosummaries.kmeans Prepare gosummaries object based on k-means results
gosummaries.MArrayLM Prepare gosummaries object based on limma results
gosummaries.matrix Prepare gosummaries object based on Multi Dimensional Scaling (MDS) results
gosummaries.prcomp Prepare gosummaries object based on PCA results
gs_kmeans 'tissue_example' is a dataset extracted from Lukk _et al_, it contains a subset of 24 samples from more than 5000 in the original article. The gene expression in all the samples is measured using Affymetrix U133A array. The dataset is a list with 2 slots 1. 'exp' - expression matrix; 2. 'annot' - annotation data frame.
gs_limma 'tissue_example' is a dataset extracted from Lukk _et al_, it contains a subset of 24 samples from more than 5000 in the original article. The gene expression in all the samples is measured using Affymetrix U133A array. The dataset is a list with 2 slots 1. 'exp' - expression matrix; 2. 'annot' - annotation data frame.
gs_limma_exp 'tissue_example' is a dataset extracted from Lukk _et al_, it contains a subset of 24 samples from more than 5000 in the original article. The gene expression in all the samples is measured using Affymetrix U133A array. The dataset is a list with 2 slots 1. 'exp' - expression matrix; 2. 'annot' - annotation data frame.
gs_pca 'tissue_example' is a dataset extracted from Lukk _et al_, it contains a subset of 24 samples from more than 5000 in the original article. The gene expression in all the samples is measured using Affymetrix U133A array. The dataset is a list with 2 slots 1. 'exp' - expression matrix; 2. 'annot' - annotation data frame.
is.gosummaries Functions for working with gosummaries object
metabolomic_example 'metabolomic_example' is a dataset extracted from York _et al_ (Metabolights ID: MTBLS30), it contains a subset of 120 wild-type samples from 4 tissues: heart, skeletal muscle, liver and brain.
metagenomic_example 'metagenomic_example' is a small sample of Human Microbiome Project 16S dataset for finding biomarkers characterizing different level of oxygen availability in different bodysites. This was downloaded from http://huttenhower.sph.harvard.edu/webfm_send/129.
panel_boxplot Panel drawing functions
panel_violin Panel drawing functions
panel_violin_box Panel drawing functions
plot.gosummaries Plot the GOsummaries figure
plotWordcloud Plot a wordcloud given words and frequencies
print.gosummaries Functions for working with gosummaries object
tissue_example 'tissue_example' is a dataset extracted from Lukk _et al_, it contains a subset of 24 samples from more than 5000 in the original article. The gene expression in all the samples is measured using Affymetrix U133A array. The dataset is a list with 2 slots 1. 'exp' - expression matrix; 2. 'annot' - annotation data frame.
[.gosummaries Functions for working with gosummaries object