CAMDAC pipeline

The entry-point to CAMDAC is the pipeline() function which expects a CamConfig() object and four CamSample() objects representing:

  • tumor : The bulk tumor sample to deconvolve
  • germline : The germline normal data for copy number calling
  • infiltrates : A proxy for the normal infiltrating cells
  • origin : A proxy for the normal cell from which the tumour originated

The same normal sample may be passed repeatedly for the germline, infiltrates or origin, depending on your experimental design. See ?pipeline for more details.

library(CAMDAC)

# Path to BAM files
tumor_bam <- system.file("testdata", "tumor.bam", package = "CAMDAC")
normal_bam <- system.file("testdata", "normal.bam", package = "CAMDAC")

# Select samples for basic tumor-normal analysis
tumor <- CamSample(id = "T", sex = "XY", bam = tumor_bam)
normal <- CamSample(id = "N", sex = "XY", bam = normal_bam)

# Configure pipeline
config <- CamConfig(
  outdir = "./results", bsseq = "rrbs", lib = "pe",
  build = "hg38", refs = "./refs", n_cores = 1, cna_caller = 'ascat'
)

# Run CAMDAC
CAMDAC::pipeline(
  tumor, germline = normal, infiltrates = normal, origin = normal, config
)

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