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 |