# Chromosome Instability Index

## Documentation for package ‘CINdex’ version 1.4.0

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

## Help Pages

clin.crc | Colon cancer clinical dataset
cnvgr.18.auto | Probe annotation file for Affymetrix Genome Wide Human SNP Array 6.0
comp.heatmap | A comprehensive heatmap function that plots Chromosome and Cytoband heatmaps
cyto.cin4heatmap | Cytoband CIN T-test output
cytobands.cin | Cytoband CIN dataset
extract.genes.in.cyto.regions | Given an input of cytobands, it outputs a list of genes that are present in the cytoband regions
geneAnno | CDS gene annotation file
grl.data | Output of segmentation algorithm
hg18.ucsctrack | Human reference annotation file
run.cin.chr | Calculate chromosome CIN
run.cin.cyto | Calculate cytoband CIN
snpgr.18.auto | Probe annotation file for Affymetrix Genome Wide Human SNP Array 6.0
ttest.cyto.cin.heatmap | Performs T test on cytoband level CIN data, and plots heatmap