Function reference • CAMDAC

All functions
`CamConfig()`	Set CAMDAC configuration
`CamSample()`	Build CAMDAC sample object
`asm_pipeline()`	Run allele-specific methylation analysis pipeline
`attach_output()`	Manually assign output file to CAMDAC sample
`cmain_bind_snps()`	Bind SNPs
`cmain_call_cna()`	Call CNA
`cmain_call_dmps()`	Call tumour-normal DMPs
`cmain_call_dmrs()`	Call tumour-normal DMRs
`cmain_count_alleles()`	Count alleles
`cmain_deconvolve_methylation()`	Deconvolve methylation
`cmain_make_methylation_profile()`	Make methylation
`cmain_make_snps()`	Make SNPs
`cmain_run_ascat()`	Run ASCAT.m
`cmain_run_battenberg()`	Run battenberg
`cwrap_asm_get_allele_counts()`	Count alleles for reads phased to SNPs in a BAM file
`download_pipeline_files()`	Download CAMDAC pipeline files
`get_reference_files()`	Get CAMDAC reference files from config
`load_cna_data()`	Parse ASCAT and bb output directories to load CNA data
`load_panel_ac_files()`	Load allele count files
`panel_asm_from_counts()`	Panel ASM from counts Basic function to create an ASM methylation panel from allele count or ASM meth files WARNING: In active development.
`panel_meth_from_beta()`	Make CAMDAC methylation panel from a matrix of beta values
`panel_meth_from_counts()`	Make CAMDAC methylation panel from allele counts Methylation fractions are obtained by summing M and UM reads across samples
`pipeline()`	CAMDAC tumor-normal pipeline
`preprocess()`	Preprocess a list of CamSample objects for analysis
`preprocess_asm()`	Preprocess a list of CamSample objects for ASM analysis

Reference