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


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Documentation for package ‘BubbleTree’ version 1.0.0

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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