Function that detects and assigns oncogenes subject to copy number amplifications, and tumor suppressor genes subject to homozygous deletions Also detects other drug targets subject to copy number amplifications

Function that detects and assigns oncogenes subject to copy number amplifications, and tumor suppressor genes subject to homozygous deletions Also detects other drug targets subject to copy number amplifications

Usage

get_oncogene_tsgene_target_sets(
  cna_df,
  transcript_overlap_pct = 100,
  log_r_gain = 0.8,
  log_r_homdel = -0.8,
  tumor_type = "Any",
  pcgr_data = NULL
)

Arguments

cna_df

data frame with copy number-transcript records

transcript_overlap_pct

minimum level of overlap for transcripts (pct)

log_r_gain

logR threshold for copy number amplifications

log_r_homdel

logR threshold for homozygous deletions

tumor_type

type of tumor

pcgr_data

PCGR data object