MDS clustering

Clusterization of the MDS disease by mutation and cytogenetics features and study of the clinical features distribution across the 11 so-found clusters.

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Requirements

Built with R version 3.5.1

• Nicola Roberts HDP R package (GitHub link) which implements the hierarchical Dirichlet process:

  devtools::install_github("nicolaroberts/hdp", build_vignettes = TRUE)

• Various R libraries:

  • ggplot2
  • reshape2
  • gridExtra
  • tibble
  • survminer
  • survival
  • glmnet
  • RColorBrewer
  • IRdisplay

todo list

• improve heatmap plot
• axes and title for each plot
• split genes by hotspots
• top genes by component
• try dataset with all genes and cytogenetics
• understand theory better
• try other clustering method
• play with hdp parameters