Aberrant epigenetic silencing of amplified genomic regions in ovarian cancer
Description
DCPM_analysis_BonitoEtAl2019.R: R script for data import and analysis SupplementaryAnalysis_BonitoEtAl2019.R: R script for analysis to produce supplementary figures and tables clinical_slide_all_ov.txt: TCGA cellularity data full450k.rds: Illumina HumanMethylation450k annotation ICGC_OV-AU_CNVbyCpG.rds: ICGC copy-number data matrix ICGC_OV-AU_GX.rds: ICGC gene expression data matrix ICGC_OV-AU_Meth.rds: ICGC DNA methylation data matrix Illumina27k_annotation2.rds: Illumina HumanMethylation27k detailed annotation Illumina27k_annotation.rds: Illumina HumanMethylation27k basic annotation sample.OV-AU.tsv: ICGC cellularity data (and sample ID table) TCGA_OV_CBS.rds: TCGA copy-number data matrix TCGA_OV_GX.rds: TCGA gene expression data matrix TCGA_OV_meth.rds: TCGA DNA methylation data matrix
Files
Steps to reproduce
DCPM_analysis.R includes all R code required to load datasets and repeat analyses