Results

CAMDAC outputs are written in the directory given by config$outdir in the format PATIENT/DATASET/SAMPLE/:

└── P
    ├── Allelecounts
    │   ├── N
    │   │   └── P.N.SNPs.CpGs.all.sorted.csv.gz
    │   └── T
    │       └── P.T.SNPs.CpGs.all.sorted.csv.gz
    ├── Copynumber
    │   ├── N
    │   │   └── P.N.SNPs.csv.gz
    │   └── T
    │       ├── ascat
    │       ├── battenberg
    │       ├── P.T.cna.txt
    │       ├── P.T.SNPs.csv.gz
    │       └── P.T.tnSNP.csv.gz
    └── Methylation
        ├── N
        │   └── P.N.m.csv.gz
        └── T
            ├── P.T.CAMDAC_annotated_DMRs.fst
            ├── P.T.CAMDAC_results_per_CpG.fst
            ├── P.T.m.csv.gz
            └── P.T.pure.csv.gz

File	Description
P.T.SNPs.CpGs.all.sorted.csv.gz	Allele counts for a sample. Generated by processing BAM file
P.T.SNPs.csv.gz	SNP counts for a sample.
P.T.cna.txt	CAMDAC CNA result
P.T.m.csv.gz	Bulk methylation data
P.T.m.pure.csv.gz	CAMDAC-deconvolved methylation data
P1.T.CAMDAC_results_per_CpG.fst	CAMDAC differentially methylated cytosines
P1.T.CAMDAC_annotated_DMRs.fst	CAMDAC differentially methylated regions

It is possible to manually override outputs for runs. See vignette("questions") for more details.