FAQs

General FAQ

What if I don’t have a CNA profile or matched germline sample? (WGBS)

Ideally, CAMDAC is run with a matched normal sample from which to derive heterozygous germline SNPs for copy number estimation. In the absence of matched normals, a panel of sex- and tissue-matched normal samples may be used by averaging DNA methylation rates from multiple patients. See vignette("experimental") for more information.

I want to run CAMDAC on something other than hg19 or hg38 (WGBS)

Please raise an issue on GitHub to request files for a new reference genome.

Can I skip steps of the analysis? (WGBS)

When calling pipeline if you do not give a normal infiltrate or cell of origin, the pipeline skips deconvolution and differential methylation respectively. This may be useful to run a quick first-pass to find and refit copy number solutions. When CAMDAC has found a solution and is rerun with the same tumor, config, and normal, the infiltrates and cell_of_origin arguments will continue the pipeline where it left off. The entire pipeline can be re-run be deleting the output directory or setting overwrite=TRUE in the CamConfig.

How do I run individual steps of the CAMDAC pipeline? (WGBS)

The simplest way is to call pipeline with overwrite=FALSE in your config, giving the right normal sample for your step. Additionally, you CamConfig must run with the same output directory.

If for any reason, you have changed the output directory structure from previous run, you can initiate CAMDAC by manually passing outputs to CamSample objects. See the vignette vignette("output") for more information.

Finally, you can run the cmain_* functions used by pipeline() directly. For example, to run the deconvolution step, you can call cmain_deconvolve_methylation().

My CNA solution wasn’t right. How can I refit with different purity and ploidy values? (WGBS)

If you want to use an external purity and ploidy solution, simply pass a CNA file that has only the purity and ploidy fields. Additionally, set refit==TRUE in the CamConfig and CAMDAC will use this to refit the sample.

Can I limit my analysis to specific regions of interest?

To analyse specific genomic regions, you may pass a BED file to CAMDAC config:

CamConfig(outdir=".", ref="./pipeline_files", regions="regions.bed")

CAMDAC will merge any overlapping regions prior to analysis.

How can I manually replace pipeline outputs? (WGBS)

If you have outputs from a previous run, you can manually assign them to a CAMDAC object. This overwrites the expected path for that output type, allowing the pipeline to run with this data instead of computing it. Use the attach_output function, passing one of three arguments:

  • counts: CAMDAC allele counts *.SNP.CpGs.all.sorted.csv.gz file
  • snps: CAMDAC sample SNP counts *.SNPs.csv.gz file
  • meth: CAMDAC bulk methylation *.m.csv.gz file
  • cna: CAMDAC CNA *.cna.txt file
  • pure: CAMDAC deconvolved methylation *.m.pure.csv.gz file

For example, to attach a previous counts file to a CAMDAC object:

library(CAMDAC)
tumor <- CamSample(id = "T", sex = "XY", bam = NULL)
config <- CamConfig(outdir = tempdir(), build="hg38", bsseq="wgbs", lib="pe")
counts_file <- system.file("testdata", "test.SNPs.CpGs.all.sorted.csv.gz", package = "CAMDAC")
tumor <- attach_output(tumor, config, "counts", counts_file)

The CAMDAC pipeline can now access the file in the expected location at config$outdir.