icgc_pcawg11_calibration

ICGC PCAWG-11 Calibration code for subclonal architecture

Run the code

	Rscript code/1_purity_ploidy.R

	Rscript code/2_mutation_assignments.R ${sample} \
		data/morris/mutation_assignment/mutation_assignment.all.${sample}.csv \
		data/vanloo_wedge/2_clustering/${sample}/${sample}_cluster_membership.txt \
		data/peifer/Mutation_Clustering/*${sample_short}_cluster_assignments.txt \
		data/peifer/Mutation_Clustering/*${sample_short}_mclusters.txt \
		data/sahinalp/citup_pilot63/samples_v1/${sample}_cluster_membership.txt

Dependencies - R packages

	Matrix
	RColorBrewer

Expected directory structure

	|-- 1_purity_ploidy
	|-- 2_mutation_assignments
	|   |-- figures
	|   |-- similarities
	|   `-- tables
	|-- code
	|-- data
	|   |-- broad
	|   |-- dirichlet_input
	|   |-- morris
	|   |   |-- mutation_assignment
	|   |   `-- mutation_relations
	|   |-- peifer
	|   |   |-- Copy_Number
	|   |   |-- Mutation_Clustering
	|   |   `-- Purity_Ploidy
	|   |-- sahinalp
	|   |   `-- citup_pilot63
	|   |       `-- samples_v1
	|   `-- vanloo_wedge
	|       |-- 1_purity_ploidy
	|       |-- 2_clustering