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CopyKit 0.1.2

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@darlanminussi darlanminussi released this 02 Feb 05:58
· 17 commits to master since this release
v.0.1.2
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Learn about vigilant mode.

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 Wei 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 the 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.
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