Results

The CAMDAC pipeline returns a structured directory at the outdir from the CamConfig() object. The pipeline returns files unique to the RRBS and WGBS modules with the general structure:

└── <CamSample.patient_id>
    ├── Allelecounts
    │   ├── <CamSample.id>
    ├── Copynumber
    │   ├── <CamSample.id>
    └── Methylation
        └── <CamSample.id>

The sections below describe each results file in more detail. Next, see vignette("questions") for frequently asked questions or vignette("experimental") for details on experimental CAMDAC features.

RRBS pipeline output

results/              
└── P                                           
    ├── Allelecounts
    │   ├── N                  
    │   │   └── P.N.SNPs.CpGs.all.sorted.RData
    │   └── T                               
    │       └── P.T.SNPs.CpGs.all.sorted.RData
    ├── Copy_number                             
    │   ├── N                        
    │   │   ├── fragment_length_histogram.pdf      
    │   │   ├── msp1_fragments_RRBS.RData
    │   │   ├── P_N_normal_SNP_data.pdf
    │   │   ├── P.N.SNPs.RData
    │   │   └── Rplots.pdf
    │   └── T
    │       ├── fragment_length_histogram.pdf
    │       ├── msp1_fragments_RRBS.RData
    │       ├── P_T_SNP_data.pdf
    │       ├── P.T.ACF.and.ploidy.txt
    │       ├── P.T.ascat.bc.RData
    │       ├── P.T.ascat.frag.RData
    │       ├── P.T.ascat.output.RData
    │       ├── P.T.ASCATprofile.png
    │       ├── P.T.ASPCF.png
    │       ├── P.T.BAF.PCFed.txt
    │       ├── P.T.germline.png
    │       ├── P.T.LogR.PCFed.txt
    │       ├── P.T.rawprofile.png
    │       ├── P.T.SNPs.RData
    │       ├── P.T.sunrise.png
    │       ├── P.T.tumour.png
    │       └── Rplots.pdf
    └── Methylation
      ├── N
      │   ├── dt_normal_m.RData
      │   └── P_N_methylation_rate_summary.pdf
      └── T
          ├── CAMDAC_DMPs.bed
          ├── CAMDAC_purified_tumour.bed
          ├── CAMDAC_results_per_CpG.RData
          ├── P_T_DMP_stats.txt
          ├── P_T_methylation_rate_summary.pdf
          ├── purified_tumour.RData
          └── tumour_versus_normal_methylomes.pdf  

File	Description
P.T.SNPs.CpGs.all.sorted.RData	Allele counts for a sample. Generated by processing BAM file
P.T.ascat.output.RData	ASCAT copy number results
P.T.ASCATprofile.png	ASCAT copy number profile
dt_normal_m.RData	Bulk normal DNA methylation data
purified_tumour.RData	CAMDAC-purified DNA methylation rates
CAMDAC_results_per_CpG.fst	CAMDAC deconvolution and differential methylation results

WGBS pipeline output

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.