Devel

[darlanminussi]

Merging copykit 0.1.2

New features

• New cell smoothing method with the function knnSmooth(). Uses k-nearest neighbors to smooth cells profiles and re-segments the datasets obtaining cleaner copy number profiles, with reduced overdispersion and improving downstream analysis. (Thanks to Runmin Weihttps://github.com/WandeRum) for the helpful discussion.)
• scquantum method is available for calcInteger() and is now a CopyKit import (scquantum is a single cell ploidy estimation tool developed by Alexander Davis)
• calcInteger() now accepts option methdo = 'metadata'. To use this option the user can add custom values of ploidy to every cell in the colData column 'ploidy' and run calcInteger(ck, method = 'metadata') to obtain the integer matrix on the CopyKit object.
• runVst allows selection of the assay for the transformation

Changes

• plotHeatmap() order_cells argument now defaults to NULL. NULL option respects the order of the CopyKit object. order_cells argument can be set to 'consensus_tree' and 'hclust'.

• Method 'scquantum' from calcInteger() adds 3 elements to the colData.

1. ploidy: contanining the inferred ploidy call for each cell
2. confidence_ratio: ratio from scquantum inferred ploidy to scquantum theoretical ploidy
3. ploidy_score: Score derived from the confidence ratio. Values closer to 0 indicate a better fit of the ploidy call

• Significance thresholds for CBS alpha segmentation and Merge levels were reduced to increase sensitivity to focal amplifications.

Removed

• option 'phylogeny' from function argument `plotHeatmap()' 'order_cells' has been removed.