Format output nucleotide counts format_output

Format output nucleotide counts format_output

format_output(
  patient_id,
  sample_id,
  sex,
  is_normal = FALSE,
  path,
  path_to_CAMDAC,
  build
)

Arguments

patient_id

Character variable containting the patient id number

sample_id

Character variable with the sample ID

sex

Character variable with the patient expressed as "XX" for female or "XY" for male.

is_normal

Logical flag set to false if the sample to be formatted is normal or tumour

path

Character path variable pointing to the desired working directory. This is where the output will be stored and should be constant for all CAMDAC functions. Do not alter the output directory structure while running CAMDAC.

path_to_CAMDAC

Character variable containting the path to the CAMDAC directory including dir name (e.g. "/path/to/CAMDAC/").

build

Character variable corresponding to the reference genome used for alignment. CAMDAC is compatible with "hg19", "hg38", "GRCH37","GRCH38". is desired in addition to GRanges object in .RData file

Value

Concatenated SNP and CpG information