Create SCNA Score Data Frame

Source: R/utility.R

Create SCNA Score Data Frame

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

Arguments

scna_genes_df

data frame of gene-level SCNAs (can be 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

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.

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.