create_camdac_config.RdSet 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
)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