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

## Documentation for package ‘HMMcopy’ version 1.4.0

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

## Help Pages

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