create_SCNA_score_df {driveR}

Create SCNA Score Data Frame

Description

Create SCNA Score Data Frame

Usage

create_SCNA_score_df(
  gene_SCNA_df,
  build = "GRCh37",
  log2_ratio_threshold = 0.25,
  MCR_overlap_threshold = 25
)

Arguments

gene_SCNA_df

data frame of gene-level SCNAs (output of create_gene_level_scna_df)

build

genome build for the SCNA segments data frame (default = "GRCh37")

log2_ratio_threshold

the log₂ ratio threshold for keeping high-confidence SCNA events (default = 0.25)

MCR_overlap_threshold

the percentage threshold for the overlap between a gene and an MCR region (default = 25). This means that if only a gene overlaps an MCR region more than this threshold, the gene is assigned the SCNA density of the MCR

Details

The function first aggregates SCNA log₂ ratio on gene-level (by keeping the ratio with the maximal |log₂| ratio over all the SCNA segments overlapping a gene). Next, it identifies the minimal common regions (MCRs) that the genes overlap and finally assigns the SCNA density (SCNA/Mb) values as proxy SCNA scores.

Value

data frame of SCNA proxy scores containing 2 columns:

gene_symbol

HGNC gene symbol

SCNA_density

SCNA proxy score. SCNA density (SCNA/Mb) of the minimal common region (MCR) in which the gene is located.