Copy number prediction with correction for GC and mappability bias for HTS data

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Documentation for package ‘HMMcopy’ version 1.32.0

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HMMcopy-package Bias-free copy number estimation and robust CNA detection in tumour samples from WGS HTS data
correctReadcount Readcount correction for GC and mappability bias
HMMcopy Bias-free copy number estimation and robust CNA detection in tumour samples from WGS HTS data
HMMcopy-dataset HMMcopy example dataset
HMMsegment Segmentation and classification of copy number profiles
normal_copy HMMcopy example dataset
plotBias Visualization functions for correctReadcount results
plotCorrection Visualization functions for correctReadcount results
plotParam Visualization functions for correctReadcount results
plotSegments Visualization functions for correctReadcount results
rangedDataToSeg WIG Output Functions
rangedDataToWig WIG Output Functions
stateCols Visualization functions for correctReadcount results
tumour HMMcopy example dataset
tumour_copy HMMcopy example dataset
tumour_param HMMcopy example dataset
tumour_reads HMMcopy example dataset
tumour_segments HMMcopy example dataset
wigsToRangedData Parsing and sorting of uncorrected read and sequence information files
wigToArray WIG Import Functions
wigToRangedData WIG Import Functions