Set CAMDAC configuration

create_camdac_config(
  outdir,
  bsseq,
  bsseq_lib,
  build,
  n_cores = 1,
  camdac_refs = NULL,
  n_seg_split = 50,
  min_mapq = 1,
  min_cov = 3,
  overwrite = FALSE,
  ascat_rho_manual = NULL,
  ascat_psi_manual = NULL,
  beaglejar = NULL
)

Arguments

outdir

A path to save CAMDAC results. The results folder structure follows the format PATIENT/DATASET/SAMPLE/. @param bsseq Bisulfite sequencing platform. Choose between "wgbs" or "rrbs". @param bsseq_lib Bisulfite sequencing library. Choose "pe" for paired end, "se" for single end. @param build Reference genome build. Choose "hg38" or "hg19". @param n_cores Number of cores to process CAMDAC data in parallel wherever possible. @param camdac_refs Path to CAMDAC reference files. If this is not given, CAMDAC searched the environment variable CAMDAC_PIPELINE_FILES. If this is not set, CAMDAC looks in the current working directory. @param n_seg_split In WGBS mode, the reference genome is split into segments for parallele processing. This parameter selects the number of segments per chromosome. @param min_mapq Minimum mapping quality filter used in cmain_allele_counts(). @param min_cov Minimum coverage filter for: DNA methylation, Normal SNP selection. @param overwrite Config to overwrite files if they already exist. @param ascat_rho_manual ASCAT rho value for refitting @param ascat_psi_manual ASCAT/Battenberg psi value for refitting @param beaglejar Path to beagle Java file for Battenberg haplotyping (WGBS only) @export