CAMDAC pipeline

The CAMDAC pipeline accepts raw data for each of the following CamSample objects:

  1. tumor - The bulk tumor sample you to deconvolve
  2. germline (optional) - Patient-matched normal data for allele-specific copy number calling. Alternatively, see using external CNA solutions below.
  3. infiltrates - Bulk methylome representing the normal infiltrating cells for deconvolution. E.g. normal adjacent tissue.
  4. origin (optional) - Bulk methylome for differential methylation calling, representing the normal cell type from which the tumour originated.

The same normal sample may be given as the germline, infiltrates or origin, depending on your experimental design.

Run the CAMDAC pipeline 

library(CAMDAC)

# Load test data
b_tumor <- system.file("testdata", "tumor.bam", package = "CAMDAC")
b_normal <- system.file("testdata", "normal.bam", package = "CAMDAC")

tumor <- CamSample(id="T", sex="XY", bam=b_tumor)
normal <- CamSample(id="N", sex="XY", bam=b_normal)
config <- CamConfig(outdir="./results", bsseq="wgbs", lib="pe", build="hg38", n_cores=10)
config <- CamConfig(
  outdir="./results_test", bsseq="wgbs", lib="pe",
  build="hg38", n_cores=10, 
  cna_caller="ascat", # Specific for test data
  min_cov=1, # Specific for test data
  cna_settings=list("rho"=.5, "psi"=2) # Specific for test data
)

When defining CamSample objects, samples must have a unique id value between runs otherwise data will be overwritten. Alternatively, users may use the patient argument to separate samples the same id.

To run the pipeline:

pipeline(
    tumor=tumor,
    germline=normal,
    infiltrates=normal,
    origin=normal,
    config=config
)

Next, see vignette("output") for a detailed summary of CAMDAC results files.