Function that annotates CNV segment files

Function that annotates CNV segment files

Usage

generate_report_data_cna(
  cna_segments_tsv,
  pcgr_data,
  sample_name,
  pcgr_config,
  oncotree,
  transcript_overlap_pct = 100
)

Arguments

cna_segments_tsv

CNV file name with chromosomal log(2)-ratio segments

pcgr_data

object with PCGR annotation data

sample_name

sample identifier

pcgr_config

Object with PCGR configuration parameters

oncotree

Data frame with phenotype terms relevant for tumor type

transcript_overlap_pct

required aberration overlap fraction (percent) for reported transcripts (default 100 percent)