Multi-Omics data integration

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Documentation for package ‘gINTomics’ version 1.3.0

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

Help Pages

create_multiassay	MultiAssayExperiment generation
dot_plotly	plotting enrichment
extract_model_res	Setting method for extracting results
extract_model_res-method	Setting method for extracting results
mirna_hsa	miRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).
mmultiassay_ov	Example data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.
MultiClass-class	MultiClass Class
MultiOmics-class	MultiOmics Class
plot_chr_distribution	plotting chr distribution
plot_heatmap	plotting heatmap
plot_network	Plotting network
plot_ridge	plotting ridge
plot_tf_distribution	plotting TF distribution
plot_venn	plotting venn
plot_volcano	plotting volcano
run_cnv_integration	Integration of expression and Copy Number Variations
run_genomic_enrich	Running genomic enrichment analysis
run_genomic_integration	Integration of expression, Copy Number Variations and methylation data
run_met_integration	Integration of expression and methylation
run_multiomics	Complete Multi-Omics integration
run_shiny	Start a Shiny application for integrated multi-omics data analysis.
run_tf_enrich	Running TF enrichment analysis
run_tf_integration	Integration of expression and Transcription Factors / Generic Regulators