run_ASCAT.m.Rdrun_ASCAT.m
run_ASCAT.m(
patient_id,
sample_id,
sex,
patient_matched_normal_id = NULL,
path,
path_to_CAMDAC,
build,
min_normal = 10,
min_tumour = 1,
n_cores = 1,
reference_panel_coverage = NULL
)Character variable containting the patient id number
Character variable with the (control or tumour) sample_id
Character variable with the patient expressed as "XX" for female or "XY" for male. This is important for copy number profiling. If sex is unknown, put "XY" for now, then look at the allelic imbalance (BAF) on X in the germline outside pseudo- autosomal regions. If there are little to no heterozygous SNPs, the sample is likely male.
Character variable with the sample ID of the matched normal control
Character path variable pointing to the desired working directory. This is where the output will be stored IMPORTANT: The function output directory will be the in the path variable working directory under "./Copy_number/sample_id/".
Character variable containting the path to the CAMDAC dir including dir name (e.g. "/path/to/CAMDAC/").
Character variable corresponding to the reference genome used for alignment. CAMDAC is compatible with "hg19", "hg38", "GRCH37","GRCH38".
Numerical value correspdonding to the minimum counts for germline SNPs to be included (default:1)
Numerical value correspdonding to the minimum counts in the tumour sample for germline SNPs to be included (default:10)
Numerical value correspdonding to the number of cores for parallel processing
Path to the reference panel for the coverage.
Three text files with all the CpG loci and their SNP and/or CpG methylation info