v0.3.1-beta

• up version and R man documentation
• squash 🐛 for undefined column when refX==FALSE
• squash 🐛 for missing fields when --MandUnormal is excluded
• determine patient sex by proportion of het chrX snps instead of raw counts

v0.3.0-beta

✨ add support for incorporation of donor sample(s) with transplant cases

v0.2.6-beta

• Add option to select best sex matched reference normal for chrX norm
• Modified jointsegsummary to be faster (using indices instead of tapply)
• procSample modified to get the cumulative segment indicator from seg
• Fixed the emcncf 'missing value where TRUE/FALSE needed' error

v0.2.2-beta

• relaxed snp-pileup DP threshold for reference normals to 1 read from 10
• disabled low coverage filtering of SNPs, ndepth parameter in call to preProcSample() can be used
• updated test data after snp-pileup changes
• bugfix for use of unmatched normals without reference data

v0.2.1-beta

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing. Package created to test FACETS with both matched and unmatched normal.

This implementation of FACETS requires a tumor sample, matched normal and user defined number of unmatched normal samples.

✨ The normal sample with computed minimal noise is selected for copy number log2 ratio calculations, while the matched normal is always selected for VALOR calculation. At present, autosomes and chromosome X are normalized separately.

🚧 (beta) infer sex from matched normal sample, and select an unmatched normal with same sex for chrX normalization.