Pre 3.0 #165
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Pre 3.0 #165
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Update parameters for sample and normal names, and reference file templates
chrX function update including fixes for raised issues
Update callSubclones function with PGA.is.clonal based on final copynumber.txt CNA file + compatibility with output.file name flexibility
Use 'PGA.is.clonal' in titles of genomewide plots
Correct error in naming the purity_ploidy file with additional "_" in samplename
Adjust chrX-based PGAclonal and automate BAFvals chrX length
Merge missing commits from Master
Merge last ChrX-related commits into Pre_3.0 branch
Conditional check on diploid length added for edge cases.
removing stretches of homozygosity from LOH calls
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