SubtypingMSc v1.0.0

Code for prostate subtyping MSc project with David Wedge

ARBS contains minor change from version provided by Atef Sahli of the University of Manchester.

Timing Model has changes from version provided by Iliana Peneva and Naser Ansari-Pour from the University of Oxford.

functions_subtyping.R must be available to other R scripts.

ARBS

Running

01_brp_sim.sh

02_dist_CI_per_bin_count_Obs-Sim.sh

03_brp_prop_20Kb.sh

Plots for distribution of categories

ar_plot.R

Heatmap of summary measurements (requires summary measurement output PPCG.txt)

ar_heatmap.R

Timing Model

Function scripts (modified from Iliana's version)

01_prepare_subclones_for_timing.R

02_01_identify_enriched_regions_gain.R

02_01_identify_enriched_regions_hd.R

02_01_identify_enriched_regions_loh.R

02_01_identify_enriched_regions.R

02_02_fdr_summary_function.R

03_prepare_enriched_regions_for_ordering.R

04_01_tree_building_functions.R

04_02_order_events_across_cohort.R

Run sequence

tm_1_run.R

tm_2_run.R

tm_3_run.R

tm_4_run.R

Used for running with seperated SCNA types

tm_2_run_gain.R

tm_2_run_hd.R

tm_2_run_loh.R

Create distance matrix

tm_cluster_generate_distance_summary.R

View hierarchical cluster of distance summary

tm_cluster_visualise.R

Get distance summary groups

tm_group_cluster.R

Get SCNA raw files from PPCGID

tm_cluster_prepare_subclone_list.R

Summaries

tm_CNA_counts.R

tm_get_cna_from_merge.R

Plot results

tm_PPCG_orderingplot.R

tm_UK_orderingplot.R

tm_ordering_plot_totals.R

Get summary measurements

Run each to generate summary.txt files

load_indel_ml_data.R

load_other_ml_data.R

load_pga_ml_data.R

load_scna_ml_data.R

load_snv_ml_data.R

load_sv_ml_data.R

Run merge_data.R to create cna_summary.txt

Clean data ahead of cluster analysis with ca_clean_data.R

Clustering Summary measurements

PCA

ca_pca.R

Comparing output of multiple runs

ca_pca_comparison.R

t-SNE

ca_tsne.R

UMAP

ca_umap.R

Comparing output of multiple runs

ca_umap_comparison.R

Compare silhouette method results from each run

ca_umap_silhouette.R

Aggregate replicates for clusterings

ca_umap_aggregate.R

Cluster aggregate umap

ca_umap_cluster.R

SOM

ca_som.R

Comparing output of multiple runs

ca_som_comparison.R

Autoencoder

ca_ae_run.R

Comparing output of multiple runs

ca_ae_comparison.R

Aggregate replicates for clusterings

ca_ae_aggregate.R

Cluster aggregate ae

ca_ae_cluster_distance.R

Generate consensus of method

Summary measurement (ARI, Fisher's Exact Test, Confusion Matrix)

cl_check_evotypes.R

Combine Methods

cl_method_aggregate.R

Feature proportion of method

cl_feature_proportion.R

Heatmap of method

cl_generic_heatmap.R

Summarise by region

cl_region.R

cl_region_aggregate.R