prepare_input_data Function — prepare_input

This function obtains the list of input data to be used in the stan model.

Usage

prepare_input_data(
  mutations,
  segments,
  purity,
  possible_k = c("2:1", "2:2", "2:0"),
  alpha = 0.05,
  min_mutations_number = 2
)

Arguments

mutations: list: output from CNAqc Mutations(x), where x is a CNAqc object
segments: list: output from CNAqc CNA(x), where x is a CNAqc object
purity: num: (type = double) sample purity between 0 and 1
possible_k: chr: "2:1" "2:2" "2:0"
alpha: num: (type double) confidence interval level to choose the data that fall in the expected binomial intervals
min_mutations_number: num: (type double) minimum number of accepted mutations for a segment to be included in the inference

Value

accepted_data: list $input_data:list: List of 7: $S: int, $N: int, $karyotype: num (0 or 1), $seg_assignment: num, $peaks:List of N of num (1:2), $NV: num, $DP: num $accepted_cna: tibble (S × 5)(S3: tbl_df/tbl/data.frame): $segment_original_indx: int, $segment_name: chr, $segment_id: num, $karyotype: chr, $chr: chr