Refactor cn-summary-workflow vignette into a broader CN-Diversity investigation workflow

Huntsmanlab / utanos

Utilities for doing analysis on shallow WGS data

https://huntsmanlab.github.io/utanos/

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Refactor cn-summary-workflow vignette into a broader CN-Diversity investigation workflow #61

Closed genomaxx closed 3 months ago

genomaxx commented 3 months ago

Refactor cn-summary-workflow vignette into a broader CN-Diversity investigation workflow. Take the current vignette and add the bits form utanos on rCN diversity plotting.

genomaxx commented 3 months ago

Related issue: #37 Both can be tackled together.

genomaxx commented 3 months ago

Address #58 at the same time.

genomaxx commented 3 months ago

[x] Refactor MakeSummaryTable function to spit out proportions as well as probabilities for both summary table and peaks table.
[x] Allow hg19, hg38, and mm10 reference genomes
[x] Because of additional dependencies add protection/checks to the function (requireNamespace() or check installed.packages() or something)

genomaxx commented 3 months ago

Issue #63 related as well. Address together.