# A method to elucidate purity and clonality in tumors using copy number ratio and allele frequency

## Documentation for package ‘BubbleTree’ version 1.0.0

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

## Help Pages

bubbletree-package | BubbleTree: a method to elucidate purity and clonality in tumors using copy number ratio and allele frequency.
addBubble | Draw a bubble
BubbleTree | BubbleTree: a method to elucidate purity and clonality in tumors using copy number ratio and allele frequency.
bubbletree | BubbleTree: a method to elucidate purity and clonality in tumors using copy number ratio and allele frequency.
calc.prev | Calculate tumor cell prevalence in a sample, an indication of sample purity
cnv.gr | A sample dataset of tumor segmented copy number variations
compareBubbles | compare bubbles from two samples
drawBranches | Plot branches of BubbleTree plot
drawBubble | Draw a bubble
getRBD | Get RBD (R-score BAF Dataframe) of the homogeneous SCNV segments
hcc.rbd.lst | Rbd data from the HCC samples
hetero.gr | BAF of the germline heterozygous loci in GRanges format
plotBubbles | Plot Bubbles