NEWS

CNVMetrics 1.5.1

NEW FEATURES

processSim() method generates simulated samples with copy number profiles derived from a specific sample.

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

calculateLog2ratioMetric() method enables log2 ratio metric calculation using similar workflow than calculateOverlapRegionsMetric() method.

SIGNIFICANT USER-VISIBLE CHANGES

plotMetric() replaces plotOverlapMetric() method. The new method can plot all metrics (state call metrics and log2 ratio metrics).
Vignette section 'Workflow for metrics calculated using the level of amplification/deletion' is complete.
New citing section in README and vignette refering to published F1000Research poster (http://www.doi.org/10.7490/f1000research.1118704.1).
Instead of calculating distance, log2 ratio metrics are calculated distance-based metrics (1/(1+distance)).

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

New website https://krasnitzlab.github.io/CNVMetrics/index.html associated to package.
Vignette section 'Workflow for metrics calculated using CNV status calls' is complete.

BUG FIXES

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

plotOneOverlapMetric() method has a new argument silent=TRUE so that the plot is not drawn by default.

BUG FIXES

plotOneOverlapMetric() method now uses sample distance for clustering as default clustering method.

NEW FEATURES

plotOneOverlapMetric() method enables plotting result of overlapping metric calculation.

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES

NEW FEATURES

Added a NEWS.md file to track changes to the package.
calculateOverlapRegionsMetric() method enables calculation of similarity metrics using overlapping amplified/deleted regions.

SIGNIFICANT USER-VISIBLE CHANGES

BUG FIXES