Build CAMDAC sample object

Build CAMDAC sample object

create_camdac_sample(
  patient_id,
  patient_sex,
  sample_id,
  sample_type,
  bam_file,
  segments_bed = NULL,
  cna = NULL
)

Arguments

patient_id

An identifier for the patient

patient_sex

The sex of the patient, "XX" or "XY". Required for CNA calling.

sample_type

Currently unused field.

bam_file

Sample BAM file

segments_bed

Optional. a BED file of genomic regions to analyse with CAMDAC. If empty, the whole genome is processed.

cna

Optional. Pre-determined allele-specific copy number data for the tumor sample. Format is a list with three entries:

  • purity fraction denoting tumor purity

  • ploidy overal tumor ploidy e.g. 3.25

  • ascna a data frame where each row is a copy number segment. Data is taken by column position where 1=chromosome, 2=start, 3=end, 4=major copy number and 5=minor copy number. If the ascna entry is left blank, the purity and ploidy entries will be used for re-fitting