Plots the coverage in a number of ways: Coverage along the chromosome, density plots of coverage for each individual copy number state (as assigned by the runHMMmethod) and coverage by GC percentage of the reads, before and after normalization.
An object of class
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Loading required package: seqinr Normalizing read counts for GC bias... Overall values for chromosome CP003467 : Median read count: 66 Median GC percentage: 0.17 Calculating per-read weight based on GC percentage... Successfully normalized chromosome CP003467 Running HMM... Analyzing chromosome CP003467 Finished setting up transition and emission matrices. Starting Viterbi algorithm... Attempting to create Viterbi matrix Positions 1 - 18800 : Most probable state = 1 Positions 18801 - 22000 : Most probable state = 2 Positions 22001 - 94200 : Most probable state = 1 Positions 94201 - 95200 : Most probable state = 0 Positions 95201 - 174014 : Most probable state = 1 Finished running Viterbi algorithm. Assigning most probable states to individual segments... Copy number analysis complete. Use print to access results.
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