Code to reproduce manuscript figures
Note that the input files are too large to host here. Please contact on obtaining the input files if you would like to rerun yourself.
The directory structure is as follows:
.
├── Figures.ipynb
├── methylationArrayData
│ ├── BLCA_450K_ZNF154.txt
│ ├── BRCA_450K_ZNF154.txt
│ ├── Bartlett
│ │ ├── 2015_Bartlett_fallopian_tube_samples_GSE74845_series_matrix_2.txt
│ │ ├── GSE72021_AverageBetaValues\ 2.csv
│ │ └── GSE72021_series_matrix.txt
│ ├── COAD_450K_ZNF154.txt
│ ├── HNSC_450K_ZNF154.txt
│ ├── KIRC_450K_ZNF154.txt
│ ├── KIRP_450K_ZNF154.txt
│ ├── LAML_450K_ZNF154.txt
│ ├── LIHC_450K_ZNF154.txt
│ ├── LUAD_450K_ZNF154.txt
│ ├── LUSC_450K_ZNF154.txt
│ ├── OV_27K_ZNF154.txt
│ ├── OV_450K_ZNF154.txt
│ ├── PAAD_450K_ZNF154.txt
│ ├── PRAD_450K_ZNF154.txt
│ ├── READ_450K_ZNF154.txt
│ ├── STAD_450K_ZNF154.txt
│ ├── TCGA_earlyStage_samples.txt
│ ├── UCEC_450K_ZNF154.txt
│ ├── noncancerDiseases
│ │ └── noncancer_disease_samples_beta_values.csv
│ └── peripheralBlood
│ ├── GSE55763_normalized_betas_ZNF154.txt
│ └── GSE55763_series_matrix.txt
├── mutationFreqs
│ ├── BLCA
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_BLCA.Mutation_Packager_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_BLCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── BRCA
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── HNSC
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_HNSC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_HNSC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── KIRC
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_KIRC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_KIRC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── KIRP
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_KIRP.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_KIRP.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── LIHC
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_LIHC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_LIHC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── LUAD
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_LUAD.Mutation_Packager_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_LUAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── OV
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_OV.Mutation_Packager_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_OV.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── PAAD
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_PAAD.Mutation_Packager_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_PAAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz
│ ├── PRAD
│ │ ├── Mutated_Genes.txt
│ │ ├── gdac.broadinstitute.org_PRAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0
│ │ └── gdac.broadinstitute.org_PRAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz
│ └── STAD
│ ├── Mutated_Genes.txt
│ ├── gdac.broadinstitute.org_STAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0
│ └── gdac.broadinstitute.org_STAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0.tar.gz
└── plasma
├── DREAMingNormalizedCounts.csv
├── KRASddPCRcounts.csv
├── TableS2_plasmaSamples.csv
├── colonNormalizedMethylatedZNFCounts.csv
├── liverNormalizedMethylatedZNFCounts.csv
├── ovarianNormalizedMethylatedZNFCounts.csv
├── pancreasEarlyNormalizedMethylatedZNFCounts.csv
└── pancreasLateNormalizedMethylatedZNFCounts.csv