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copykit devel

copykit 0.1.3

Bug Fixes Fixed gamma segmentation argument not being used when applying multipcf segmentation #94 Fixed 'smoothed_bincounts' check #97. Thanks @Puriney

Fixed installation of multipcf after Bioconductor {{copynumber}} package deprecation.

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.

Bug Fixes

  • Fixed error in plotGeneCopy not returning plots with geom violin and barplot. (Thanks to @Romeo1-1)
  • Fixed error in plotGeneCopy with duplicated sample names on a merged object. Now it warns the user of merged sample names. (Thanks to @Romeo1-1)
  • Allowing control of parameter merge_levels_alpha on runVarbin() and runSegmentation() to control the significance level of merge levels when merging not significant segments.

copykit 0.1.1

  • Reduced quality of heatmap raster that could quickly use all magick cache
  • Fixed hg38 scaffold issue for lower resolutions 500kb, 1Mb and 2.8Mb in which the quality control of low quality bins was too strict and causing problems especially on chromosome X. (Thanks to @Romeo1-1)

copykit 0.1.0

  • CopyKit goes 0.1.0.

copykit 0.0.0.9036

  • Added a NEWS.md file to track changes to the package.

copykit 0.0.0.9037

  • Changed values of resolution argument in runVarbin() to more accurately reflect the variable genomic scaffolds. Resolutions are: '55kb', '110kb', '195kb', '220kb', '280kb', '500kb', '1Mb', '2.8Kb'

copykit 0.0.0.9038

  • Adding PCA and PCA related functions
  • runPca()
  • plotPca()
  • plotScree()
  • Clustering functions can use n dimensions with either UMAP or PCA
  • added argument ncomponents to findSuggestedK() and findClusters

copykit 0.0.0.9039

  • Fixed a critical bug in runSegmentation to set the correct log base call during merge levels.

copykit 0.0.0.9040

  • Adding raster arguments to plotHeatmap().