# Retroviral Integration Pattern Analysis Tool (RIPAT)

## Documentation for package ‘RIPAT’ version 1.4.0

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

## Help Pages

annoByCpG | Annotate integration sites by CpG sites.
annoByGene | Annotate integration sites by genes and TSSs.
annoByRepeat | Annotate integration sites by repeats and microsatellites.
annoByVar | Annotate integration sites by clinical variants.
blast_gene | Integration site annotation by gene data
blast_obj | Retroviral vector integration site object
cpg_exam_db | Data file for annoByCpG vignette
drawingKaryo | Draw the karyogram plot.
gene_exam_db | Data file for annoByGene vignette
makeData | Make data files for RIPAT.
makeDocument | Make the result object and document.
makeInputObj | Make the retroviral vector integration site object.
makeInputObj2 | Make the retroviral vector integration site object.
micro_exam_db | Data file for annoByRepeat vignette
repeat_exam_db | Data file for annoByRepeat vignette
tss_exam_db | Data file for annoByGene vignette
var_exam_db | Data file for annoByVar vignette