Function reference • CAMDAC

All functions
`CamConfig()`	Set CAMDAC configuration
`CamSample()`	Build CAMDAC sample object
`LogR_correction()`	LogR_correction
`annotate_copy_number()`	Assign copy number calls
`ascat.m.plotRawData()`	ascat.m.plotRawData
`ascat.m.plotSegmentedData()`	ascat.m.plotSegmentedData
`asm_pipeline()`	Run allele-specific methylation analysis pipeline
`attach_output()`	Manually assign output file to CAMDAC sample
`bin_CpGs()`	Cluster CpGs into annotated bins
`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
`compute_tumour_methylome()`	Compute the tumour methylation rate
`cwrap_asm_get_allele_counts()`	Count alleles for reads phased to SNPs in a BAM file
`download_pipeline_files()`	Download CAMDAC pipeline files
`format_methylation_df()`	Format methylation rates `format_methylation_df`
`format_output()`	Format output nucleotide counts `format_output`
`get_DMPs()`	Get DMPs
`get_DMRs()`	Assign bins
`get_allele_counts()`	Compile allele counts at SNPs and at CpGs for bisulfite sequencing data `get_allele_counts`
`get_differential_methylation()`	Perform differential methylation analysis on deconvolute tumour methylation rates
`get_msp1_fragments()`	get_msp1_fragments
`get_pure_tumour_methylation()`	Deconvolve the pure tumour methylation rate from bisulfite sequencing data
`get_reference_files()`	Get CAMDAC reference files from config
`intervalWidth()`	@param ICDFname is R's name for the inverse cumulative density function of the distribution.
`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
`pipeline_tumor_normal()`	Call CAMDAC for a tumor and patient-matched normal sample
`plot_BAF_and_LogR()`	Plot BAF and logR profiles with ggplot
`plot_SNP_info()`	Plot SNP data summary and QC
`plot_methylation_info()`	Plot Methylation
`plot_normal_SNP_info()`	Plot plots SNP QC
`preprocess()`	Preprocess a list of CamSample objects for analysis
`preprocess_asm()`	Preprocess a list of CamSample objects for ASM analysis
`remove_low_cov_singletons()`	remove_low_cov_singletons
`run_ASCAT.m()`	Obtain allele-specific copy number profiles, tumour purity and plot SNP data
`run_methylation_data_processing()`	Filter bulk tumour and normal methylation data, get methylation rate highest density interval (HDI) and plot raw methylation info `run_methylation_data_processing`
`sort_genomic_dt()`	Sort a data table with genomic coordinates

Reference

All functions